Sam:LabNotes/Microbiome-new/2011-4-14
Jump to navigation
Jump to search
Quantify low quality E.coli reads from Ecoli SAGs sequencing results
Background
- Since bowtie mapping is very stringent, some E.coli reads (assuming they are low-quality E.coli reads) are not able to be mapped.
- Total reads = mappled E.coli reads + non-mapped E.coli reads + non-mapped non-E.coli reads
- The objective here is to quantify how many of those non-mapped E.coli reads.
- We can't not directly BLASTN all of the failed-to-align reads since it will take extremely long time (> 1 week) using genemapster.
Possible approaches
BLATing failed-to-align reads
- BLAT failed-to-align reads to E.coli genome -> output in BLAST-output format -> MEGAN extraction of E.coli related reads and get quantitative information.