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===Discussions=== *Most of fail-to-align reads can only be assembled to short contigs (under k-mer 27) *The contigs assembled from fail-to-aligned reads(against E.coli template) '''contain a significant amount of human DNA contigs'''. γ ID1 ID2 ID3 ID4 ID5 ID6 ID7 ID8 ----------------------------------------------------------- Homo hits N/A 22 0 25 155 86 35 83 All hits N/A 75 15 106 200 145 56 120 (%) 29.3% 23.6% 77.5% 59.3% 62.5% 69.1% All failed-to-align contig hit *'''A certain level fail-to-align contigs also match E.coli genome (e.g. ID-3 and ID-8)'''. It is unknown why some E.coli reads are failed to map to E.coli genome in bowtie. ***Sequencing error => mis-match >3bp => fail to meet mapping criteria in bowtie? ***Chimeric junction in these "single-end" reads? *ID-1 showed no BLAST hit using length>300 contigs. I tried using length>200 contigs for BLAST but it still came out no hit. *I am thinking that maybe it's a better idea to '''use MEGAN metagenomics tool for analyzing these fail-to-align reads''' directly, which it can draw a taxonomic distribution plot easily.
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