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Summary
Started job onStarted mapping onFinished onMapping speed, Million of reads per hourNumber of input readsAverage input read lengthUniquely mapped reads numberUniquely mapped reads %Average mapped lengthNumber of splices: TotalNumber of splices: Annotated (sjdb)Number of splices: GT/AGNumber of splices: GC/AGNumber of splices: AT/ACNumber of splices: Non-canonicalMismatch rate per base, %Deletion rate per baseDeletion average lengthInsertion rate per baseInsertion average lengthNumber of reads mapped to multiple loci% of reads mapped to multiple lociNumber of reads mapped to too many loci% of reads mapped to too many loci% of reads unmapped: too many mismatches% of reads unmapped: too short% of reads unmapped: otherNumber of chimeric reads% of chimeric reads
sample_idmap_step
ECHO1710-A07_lncRNA_A07-05rRNAJan 03 18:04:57Jan 03 18:04:58Jan 03 19:10:0973.7280087412257522520.07%254.73553014823401710.09%0.01%1.160.00%2.132302064.03%4640750.58%0.00%1.58%93.75%00.00%
genomeJan 03 20:51:59Jan 03 20:53:52Jan 04 00:03:2824.31768236412562297804029.91%265.954267930368199238037734024576454162670.68%0.05%2.340.03%2.7548992066.38%20481572.67%0.00%58.92%2.13%00.00%
circRNAJan 04 03:18:01Jan 04 03:18:03Jan 04 06:43:3314.34491211032472278020.46%209.38336540214787645305861.35%0.03%2.510.01%1.715845783.23%1829790.37%0.00%95.11%0.83%00.00%
ECHO1710-A07_lncRNA_A07-07rRNAJan 03 19:44:12Jan 03 19:44:12Jan 03 20:43:1578.0376796788249381550.05%246.2238501639121290.10%0.01%1.220.00%114976701.95%3366060.44%0.00%1.16%96.40%00.00%
genomeJan 03 22:23:12Jan 03 22:24:09Jan 04 01:35:3723.59752699172481027529813.65%255.022715921238995924588062175254142299490.77%0.06%2.580.03%2.9847661436.33%24207273.22%0.00%74.62%2.18%00.00%
circRNAJan 04 04:29:14Jan 04 04:29:16Jan 04 08:46:2614.08603537642472004060.33%184.23377300154119623359701.55%0.03%2.440.01%1.6919822303.28%2333400.39%0.00%94.95%1.05%00.00%
ECHO1710-A07_lncRNA_A07-08rRNAJan 03 18:04:57Jan 03 18:04:58Jan 03 19:06:2370.6372298680248800930.11%258.621729078837305680.08%0.01%1.40.00%1.6159037818.17%4452340.62%0.00%2.68%88.43%00.00%
genomeJan 03 20:43:43Jan 03 20:45:29Jan 03 22:53:4231.05663461792441384853620.87%266.687576282714393672451136150679122617510.60%0.04%2.350.02%2.6155900578.43%33260995.01%0.00%61.39%4.30%00.00%
circRNAJan 04 02:28:21Jan 04 02:28:24Jan 04 05:54:3713.69470539432373130490.67%209.466449603525896462596131.11%0.02%2.580.01%2.336923607.85%4249130.90%0.00%89.20%1.38%00.00%
ECHO1710-A07_lncRNA_A07-09rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:11:4573.2881563909253452480.06%257.88733031614102760.09%0.01%1.230.00%1.6530755253.77%4358890.53%0.00%1.33%94.30%00.00%
genomeJan 03 21:15:05Jan 03 21:16:23Jan 03 23:57:0529.29784592122521189218315.16%268.133641476335798134292652571752161812780.59%0.04%2.310.02%2.6144791005.71%25981753.31%0.00%73.34%2.48%00.00%
circRNAJan 04 03:34:44Jan 04 03:34:47Jan 04 08:54:0111.69622010572492061210.33%205.085316603497170248492511.36%0.02%2.220.01%2.0323878893.84%2768270.45%0.00%94.61%0.78%00.00%
ECHO1710-A07_lncRNA_A07-10rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:29:5170.4699684977270837680.08%243.191353016888503000.08%0.02%1.460.00%153861595.40%2368930.24%0.00%2.07%92.20%00.00%
genomeJan 03 22:10:53Jan 03 22:11:59Jan 04 02:11:3523.6942447592703018617732.03%2757990913751198776630035760275652627430.57%0.04%1.870.02%2.2441456174.40%8712510.92%0.00%62.00%0.65%00.00%
circRNAJan 04 04:41:45Jan 04 04:41:50Jan 04 09:34:0712.33600697182651202690.20%227.886150171146613962990.92%0.03%2.370.01%2.14908290.15%86460.01%0.00%99.46%0.18%00.00%
ECHO1710-A07_lncRNA_A07-11rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 18:59:2185.3477352392223194370.03%252.9256001435803590.13%0.00%1.10.00%1.1113751791.78%2436750.32%0.00%0.90%96.98%00.00%
genomeJan 03 19:46:58Jan 03 19:49:21Jan 03 22:46:4925.687596674722244807815.90%235.11118829410646371099830102761631765570.69%0.04%2.650.02%2.83912618912.01%41318415.44%0.00%71.94%4.70%00.00%
circRNAJan 04 02:04:44Jan 04 02:04:51Jan 04 07:18:2912.06630346782242198280.35%159.0840581013623008389111.58%0.02%2.430.01%3.8249750647.89%6109310.97%0.00%89.41%1.38%00.00%
ECHO1710-A07_lncRNA_A07-12rRNAJan 03 19:37:31Jan 03 19:37:31Jan 03 20:42:0172.6378078939257628140.08%254.121286034943005070.07%0.01%1.20.00%1.1747615886.10%5301800.68%0.00%2.21%90.93%00.00%
genomeJan 03 22:17:30Jan 03 22:19:01Jan 04 03:28:3314.21732827612551097785014.98%267.35529400520129252859994939844901895130.56%0.03%2.230.02%2.6635230784.81%18271312.49%0.00%76.18%1.54%00.00%
circRNAJan 04 05:58:39Jan 04 05:58:44Jan 04 09:16:3517.86588974822512771210.47%219.23509703875112918300751.03%0.02%2.160.02%3.213356262.27%1522380.26%0.00%96.47%0.53%00.00%
ECHO1710-A07_lncRNA_A07-14rRNAJan 03 19:42:06Jan 03 19:42:06Jan 03 20:50:3075.7486345723278257280.03%256.94590027221101070.11%0.01%1.10.00%127812763.22%2193210.25%0.00%0.93%95.56%00.00%
genomeJan 03 22:25:35Jan 03 22:27:21Jan 04 03:11:3817.63835515492782328513227.87%280.723911023350339236057213388245062669140.54%0.05%2.20.02%2.6129887313.58%11142741.33%0.00%66.11%1.11%00.00%
circRNAJan 04 04:51:02Jan 04 04:51:04Jan 04 08:19:2516.52573744452761442400.25%233.6613744024624934107851.09%0.03%2.480.01%2.057085021.23%865660.15%0.00%97.97%0.39%00.00%
ECHO1710-A07_lncRNA_A07-17rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:31:2771.4110293583228373290.01%253.5129018740370.13%0.00%1.180.00%18048470.78%799190.08%0.00%0.26%98.87%00.00%
genomeJan 03 21:45:37Jan 03 21:46:41Jan 04 02:31:0521.5510212716028374037227.25%278.58152649013833411434373129801826773110.53%0.04%2.010.02%2.319705500.95%3675000.36%0.00%91.14%0.30%00.00%
circRNAJan 04 04:52:05Jan 04 04:52:10Jan 04 10:51:3515.6693783076283772650.08%239.12781602620161150340.86%0.02%1.590.02%32315640.25%255800.03%0.00%99.56%0.08%00.00%
ECHO1710-A07_lncRNA_A07-18rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:25:0770.5694255233269441720.05%247.43693026327701530.12%0.01%1.140.00%1.7334315673.64%5171530.55%0.00%1.35%94.42%00.00%
genomeJan 03 21:40:01Jan 03 21:41:14Jan 04 01:00:3027.349079376326869245087.63%254.41179151616811731711340135011683649920.59%0.03%1.90.01%2.2218695262.06%9205351.01%0.00%88.67%0.63%00.00%
circRNAJan 04 05:49:07Jan 04 05:49:13Jan 04 10:21:2718.33831771422681930900.23%174.8410571019383712282401.09%0.01%1.850.00%1.227323320.88%929170.11%0.00%98.59%0.19%00.00%
ECHO1710-A07_lncRNA_A07-S01-01rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:02:3874.6471739480247153620.02%230.931880127130480.12%0.02%2.350.00%914160791.97%2602220.36%0.00%0.91%96.73%00.00%
genomeJan 03 20:10:00Jan 03 20:12:00Jan 03 22:08:0836.337031727524739848565.67%277.91211643620312792059024126302296424860.49%0.02%1.790.01%1.7815797022.25%11821711.68%0.00%88.45%1.96%00.00%
circRNAJan 04 00:51:33Jan 04 00:51:38Jan 04 07:09:1810.364810712245691950.11%216.4691180666971383421.06%0.02%2.490.02%2.4816323622.52%1560970.24%0.00%96.24%0.89%00.00%
ECHO1710-A07_lncRNA_A07-S01-02rRNAJan 03 18:04:57Jan 03 18:04:58Jan 03 19:00:4275.6770288664249173430.02%230.34154010220500.12%0.01%1.090.00%12.615992462.28%2884790.41%0.00%0.97%96.32%00.00%
genomeJan 03 19:51:13Jan 03 19:52:29Jan 03 21:48:3735.486868203524849060707.14%278.36323708431283493158983227092918524740.46%0.02%1.550.01%1.6616787592.44%12104051.76%0.00%86.77%1.88%00.00%
circRNAJan 03 23:27:01Jan 03 23:27:03Jan 04 03:57:2513.7962155864245822360.13%217.0210044087216512088871.01%0.02%2.590.01%1.8915843882.55%1485440.24%0.00%96.25%0.83%00.00%
ECHO1710-A07_lncRNA_A07-S01-03rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:01:3071.2467124822252233160.03%236.3614508080570.11%0.01%1.060.00%122007433.28%2694100.40%0.00%1.11%95.17%00.00%
genomeJan 03 19:49:56Jan 03 19:51:32Jan 03 21:42:2235.146491391825151154097.88%278.55354364934209163454444243974015607930.46%0.02%1.780.01%1.7214117862.17%8052991.24%0.00%87.47%1.24%00.00%
circRNAJan 03 22:54:38Jan 03 22:54:46Jan 04 03:49:4411.8958440425248948940.16%222.44972001578178079640.92%0.03%2.350.01%2.229636881.65%888690.15%0.00%97.44%0.59%00.00%
ECHO1710-A07_lncRNA_A07-S01-04rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:02:3071.6768726326257184060.03%232.812805640680.12%0.01%1.090.00%4.8622694143.30%2345200.34%0.00%1.04%95.29%00.00%
genomeJan 03 19:49:56Jan 03 19:52:01Jan 03 21:48:1934.2866452833256714218510.75%272.813742964355355336012172807051761085010.58%0.04%2.220.02%2.3721324203.21%12894021.94%0.00%81.98%2.13%00.00%
circRNAJan 03 23:06:59Jan 03 23:07:03Jan 04 04:55:389.86572595702541176400.21%221.65136210173326131115960.91%0.03%1.960.01%1.5116652342.91%1593730.28%0.00%95.35%1.26%00.00%
ECHO1710-A07_lncRNA_A07-S01-05rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 18:58:5273.0565619298248188480.03%228.513106580580.09%0.01%1.110.00%414807312.26%1961450.30%0.00%1.06%96.36%00.00%
genomeJan 03 19:46:56Jan 03 19:48:55Jan 03 21:41:0834.296413158924738648486.03%269.83263555325359012563684203851388500960.51%0.02%1.840.01%1.8920536693.20%15764872.46%0.00%85.26%3.06%00.00%
circRNAJan 03 22:33:06Jan 03 22:33:11Jan 04 02:36:4714.3658284780246905460.16%204.9115404011431902140691.08%0.02%2.050.01%2.1924701834.24%2385160.41%0.00%94.11%1.09%00.00%
ECHO1710-A07_lncRNA_A07-S01-06rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:04:5067.4167262003246629200.09%233.6839102442701200.09%0.01%1.680.00%5.9238866045.78%6452420.96%0.00%2.32%90.85%00.00%
genomeJan 03 20:08:02Jan 03 20:09:44Jan 03 22:01:1134.1633393842431148545818.13%271.716779990650042665816845288355431398800.50%0.03%2.060.01%2.0440985526.47%27183314.29%0.00%66.83%4.27%00.00%
circRNAJan 03 23:27:24Jan 03 23:27:31Jan 04 03:54:4110.76479020692362243950.47%217.433326004360633263280040.97%0.03%3.070.01%2.2733457646.98%3214990.67%0.00%90.26%1.62%00.00%
ECHO1710-A07_lncRNA_A07-S01-07rRNAJan 03 19:37:32Jan 03 19:37:32Jan 03 20:22:5488.767063532256183000.03%236.913006150640.10%0.01%1.620.00%5.3316525852.46%2756460.41%0.00%1.04%96.06%00.00%
genomeJan 03 22:13:15Jan 03 22:15:08Jan 04 00:43:0726.526540320925560727689.29%276.47301382828822042922887202272341683730.51%0.03%1.910.01%2.1420465943.13%13108702.00%0.00%83.11%2.47%00.00%
circRNAJan 04 04:24:28Jan 04 04:24:31Jan 04 09:11:181257345191253687640.12%213.2187740972246775491.03%0.04%3.10.01%2.3913286862.32%1283760.22%0.00%96.54%0.80%00.00%
ECHO1710-A07_lncRNA_A07-S01-08rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 18:54:2073.7160649326245328200.05%236.112080101220850.11%0.01%1.380.00%2.6423005663.79%3444470.57%0.00%1.67%93.91%00.00%
genomeJan 03 19:46:14Jan 03 19:48:58Jan 03 21:38:1832.0158332968243761136313.05%267.734233781399844740633582954261471347340.60%0.04%2.520.02%2.6434025125.83%22190813.80%0.00%72.88%4.44%00.00%
circRNAJan 03 22:32:29Jan 03 22:32:39Jan 04 05:21:416.96474334342401448790.31%205.58258200233819066232261.14%0.02%2.330.01%2.432352816.82%3097850.65%0.00%90.48%1.74%00.00%
ECHO1710-A07_lncRNA_A07-S01-09rRNAJan 03 18:04:58Jan 03 18:04:58Jan 03 19:02:5766.9564696954264331810.05%236.6523501101401110.09%0.01%1.40.00%2.237528885.80%3413290.53%0.00%1.75%91.87%00.00%
genomeJan 03 20:51:25Jan 03 20:52:53Jan 03 22:31:0137.26609358572631309747821.49%281.658087665778074478746825835884081462170.46%0.03%1.840.01%1.8423029953.78%8531451.40%0.00%72.21%1.12%00.00%
circRNAJan 04 00:59:34Jan 04 00:59:41Jan 04 06:24:418.42456302702562049190.45%232.96158440267656910125890.78%0.04%3.40.01%2.147493051.64%686080.15%0.00%97.05%0.71%00.00%
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "summary = pd.read_table('mapping_star.txt', sep='\\t')\n", "summary.set_index(['sample_id', 'map_step'], inplace=True)\n", "display(summary.style.set_caption('Summary'))" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Read counts summary
Number of input readsUniquely mapped reads numberNumber of reads mapped to multiple lociNumber of reads mapped to too many lociNumber of reads unmapped: too many mismatchesNumber of reads unmapped: too shortNumber of reads unmapped: other
sample_idmap_step
ECHO1710-A07_lncRNA_A07-05rRNA800874125225232302064640750126538175081948
genome7682364122978040489920620481570452644891636343
circRNA491211032278021584578182979046719081407705
ECHO1710-A07_lncRNA_A07-07rRNA76796788381551497670336606089084274032103
genome7526991710275298476614324207270561664121640884
circRNA603537642004061982230233340057305898633714
ECHO1710-A07_lncRNA_A07-08rRNA722986808009359037814452340193760463933722
genome6634617913848536559005733260990407299192852885
circRNA470539433130493692360424913041972117649344
ECHO1710-A07_lncRNA_A07-09rRNA815639094524830755254358890108479976914766
genome7845921211892183447910025981750575419861945788
circRNA622010572061212387889276827058848420485168
ECHO1710-A07_lncRNA_A07-10rRNA996849778376853861592368930206347991909548
genome94244759301861774145617871251058431750612590
circRNA60069718120269908298646059745341108125
ECHO1710-A07_lncRNA_A07-11rRNA77352392194371375179243675069617175016349
genome759667474480781912618941318410546504773570437
circRNA630346782198284975064610931056359305869878
ECHO1710-A07_lncRNA_A07-12rRNA780789396281447615885301800172554470997179
genome7328276110977850352307818271310558268071128554
circRNA588974822771211335626152238056818400312156
ECHO1710-A07_lncRNA_A07-14rRNA86345723257282781276219321080301582511972
genome835515492328513229887311114274055235929927422
circRNA5737444514424070850286566056209743223760
ECHO1710-A07_lncRNA_A07-17rRNA1029358327329804847799190267633101772657
genome1021271607403722970550367500093078693306381
circRNA93783076772652315642558009337043075026
ECHO1710-A07_lncRNA_A07-18rRNA942552334417234315675171530127244588995790
genome9079376369245081869526920535080506829572000
circRNA8317714219309073233292917082004344158036
ECHO1710-A07_lncRNA_A07-S01-01rRNA71739480153621416079260222065282969393599
genome703172753984856157970211821710621956291378218
circRNA64810712691951632362156097062373829576815
ECHO1710-A07_lncRNA_A07-S01-02rRNA70288664173431599246288479068180067702041
genome686820354906070167875912104050595954011291222
circRNA62155864822361584388148544059825019515893
ECHO1710-A07_lncRNA_A07-S01-03rRNA67124822233162200743269410074508563882693
genome6491391851154091411786805299056780204804932
circRNA584404259489496368888869056944350344798
ECHO1710-A07_lncRNA_A07-S01-04rRNA68726326184062269414234520071475365489316
genome664528337142185213242012894020544780321415445
circRNA572595701176401665234159373054596999721470
ECHO1710-A07_lncRNA_A07-S01-05rRNA65619298188481480731196145069556463230755
genome641315893864848205366915764870546785921962426
circRNA58284780905462470183238516054851806635304
ECHO1710-A07_lncRNA_A07-S01-06rRNA672620036292038866046452420156047861107529
genome6333938411485458409855227183310423297102704591
circRNA479020692243953345764321499043236407776013
ECHO1710-A07_lncRNA_A07-S01-07rRNA67063532183001652585275646069746064421228
genome654032096072768204659413108700543566061615459
circRNA57345191687641328686128376055361047458761
ECHO1710-A07_lncRNA_A07-S01-08rRNA606493263282023005663444470101284356955782
genome583329687611363340251222190810425130672589983
circRNA474334341448793235281309785042917771825341
ECHO1710-A07_lncRNA_A07-S01-09rRNA646969543318137528883413290113219659437091
genome60935857130974782302995853145044001782682481
circRNA4563027020491974930568608044284177323974
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "summary_counts = summary.reindex(columns=[\n", " 'Number of input reads', \n", " 'Uniquely mapped reads number',\n", " 'Number of reads mapped to multiple loci', \n", " 'Number of reads mapped to too many loci'\n", " ])\n", "for item in ('too many mismatches', 'too short', 'other'):\n", " summary_counts['Number of reads unmapped: {}'.format(item)] = \\\n", " (summary['% of reads unmapped: {}'.format(item)]\\\n", " .str.strip('%').astype('float')*0.01*summary_counts['Number of input reads']).astype('int')\n", "\n", "display(summary_counts.style.set_caption('Read counts summary'))" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Read percent summary
Uniquely mapped reads numberNumber of reads mapped to multiple lociNumber of reads mapped to too many lociNumber of reads unmapped: too many mismatchesNumber of reads unmapped: too shortNumber of reads unmapped: other
sample_idmap_step
ECHO1710-A07_lncRNA_A07-05rRNA0.0654.0330.5790.0001.58093.750
genome29.9106.3772.6660.00058.9202.130
circRNA0.4643.2260.3730.00095.1100.830
ECHO1710-A07_lncRNA_A07-07rRNA0.0501.9500.4380.0001.16096.400
genome13.6516.3323.2160.00074.6202.180
circRNA0.3323.2840.3870.00094.9501.050
ECHO1710-A07_lncRNA_A07-08rRNA0.1118.1660.6160.0002.68088.430
genome20.8738.4265.0130.00061.3904.300
circRNA0.6657.8470.9030.00089.2001.380
ECHO1710-A07_lncRNA_A07-09rRNA0.0553.7710.5340.0001.33094.300
genome15.1575.7093.3110.00073.3402.480
circRNA0.3313.8390.4450.00094.6100.780
ECHO1710-A07_lncRNA_A07-10rRNA0.0845.4030.2380.0002.07092.200
genome32.0304.3990.9240.00062.0000.650
circRNA0.2000.1510.0140.00099.4600.180
ECHO1710-A07_lncRNA_A07-11rRNA0.0251.7780.3150.0000.90096.980
genome5.89812.0135.4390.00071.9404.700
circRNA0.3497.8930.9690.00089.4101.380
ECHO1710-A07_lncRNA_A07-12rRNA0.0806.0980.6790.0002.21090.930
genome14.9804.8082.4930.00076.1801.540
circRNA0.4712.2680.2580.00096.4700.530
ECHO1710-A07_lncRNA_A07-14rRNA0.0303.2210.2540.0000.93095.560
genome27.8693.5771.3340.00066.1101.110
circRNA0.2511.2350.1510.00097.9700.390
ECHO1710-A07_lncRNA_A07-17rRNA0.0070.7820.0780.0000.26098.870
genome7.2500.9500.3600.00091.1400.300
circRNA0.0820.2470.0270.00099.5600.080
ECHO1710-A07_lncRNA_A07-18rRNA0.0473.6410.5490.0001.35094.420
genome7.6272.0591.0140.00088.6700.630
circRNA0.2320.8800.1120.00098.5900.190
ECHO1710-A07_lncRNA_A07-S01-01rRNA0.0211.9740.3630.0000.91096.730
genome5.6672.2471.6810.00088.4501.960
circRNA0.1072.5190.2410.00096.2400.890
ECHO1710-A07_lncRNA_A07-S01-02rRNA0.0252.2750.4100.0000.97096.320
genome7.1432.4441.7620.00086.7701.880
circRNA0.1322.5490.2390.00096.2500.830
ECHO1710-A07_lncRNA_A07-S01-03rRNA0.0353.2790.4010.0001.11095.170
genome7.8802.1751.2410.00087.4701.240
circRNA0.1621.6490.1520.00097.4400.590
ECHO1710-A07_lncRNA_A07-S01-04rRNA0.0273.3020.3410.0001.04095.290
genome10.7483.2091.9400.00081.9802.130
circRNA0.2052.9080.2780.00095.3501.260
ECHO1710-A07_lncRNA_A07-S01-05rRNA0.0292.2570.2990.0001.06096.360
genome6.0263.2022.4580.00085.2603.060
circRNA0.1554.2380.4090.00094.1101.090
ECHO1710-A07_lncRNA_A07-S01-06rRNA0.0945.7780.9590.0002.32090.850
genome18.1336.4714.2920.00066.8304.270
circRNA0.4686.9850.6710.00090.2601.620
ECHO1710-A07_lncRNA_A07-S01-07rRNA0.0272.4640.4110.0001.04096.060
genome9.2853.1292.0040.00083.1102.470
circRNA0.1202.3170.2240.00096.5400.800
ECHO1710-A07_lncRNA_A07-S01-08rRNA0.0543.7930.5680.0001.67093.910
genome13.0485.8333.8040.00072.8804.440
circRNA0.3056.8210.6530.00090.4801.740
ECHO1710-A07_lncRNA_A07-S01-09rRNA0.0515.8010.5280.0001.75091.870
genome21.4943.7791.4000.00072.2101.120
circRNA0.4491.6420.1500.00097.0500.710
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "summary_percent = summary_counts.copy()\n", "summary_percent = 100.0*summary_percent.div(summary_percent['Number of input reads'], axis=0)\n", "summary_percent.drop(columns=['Number of input reads'], inplace=True)\n", "display(summary_percent.style.format(gradient_func).set_caption('Read percent summary'))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.7" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": false } }, "nbformat": 4, "nbformat_minor": 2 }