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==Discussions== *I found that there is a inconsistency between the bowtie mapping and 1000-raw_read_blastn results. **It is weird that in some libraries the E.coli read ration(%) were even lower then that in bowtie mapping results. **It is unlikely due to the BLASTN stringency. BLASTN should be less rigid than bowtie since BLASTn reports any E.coli hit even it is a not a strain-specific E.coli read (e.g. E.coli DH1..). *I doubt if the sample size plays a factor on this matter. I noticed that in the Illumina library ID3 and ID8, there are very high proportion of E.coli reads identified by blastn but the reads were fallen in the failed-to-align category. However, the original failed-to-align reads (in bowtie mapping) are much fewer in ID3 and ID8 libraries. *I probably should not use the fixed sample size for taxonomic analysis on raw reads and failed-to-aligned reads.
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