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==Testing using less-stringent report suppression setting on bowtie mapping== *I noticed that the genome coverage calculation script (Read2coverage-kz-3) calculate the coverage from bowtie.out file, however the bowtie.out file only report unique mapped reads (confirmed on http://genome-tech.ucsd.edu/LabNotes/index.php/Sam:LabNotes/Microbiome-new/2010-12-13). **I guess there are genome coverages not counted if they are from non-unique mapped reads, since non-uniqe mapped reads were not reported in bowtie.out. ===Re-analyze genome coverage using new scripts with less-stringent report suppression=== *test data set: s_4_ID6.txt from SE data set (HL083 E.coli SAGs) **This data set has the highest genome coverage than others. *'''Read2coverage-kz-3-suppress_5''' **(allow reporting 5 alignments from 1 read) *Results # reads processed: 2372473 # reads with at least one reported alignment: 1512449 (63.75%) # reads that failed to align: 512805 (21.61%) # reads with alignments suppressed due to -m: 347219 (14.64%) Reported 1512449 alignments to 1 output stream(s) total bps coverred = 1824363 *'''Read2coverage-kz-3-suppress_10''' **(allow reporting 10 alignments from 1 read) *Results # reads processed: 2372473 # reads with at least one reported alignment: 1857421 (78.29%) # reads that failed to align: 512805 (21.61%) # reads with alignments suppressed due to -m: 2247 (0.09%) Reported 1857421 alignments to 1 output stream(s) total bps coverred = 1869404
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