Sam:LabNotes/Microbiome-new/2011-4-14

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Revision as of 07:49, 18 April 2011 by >Sam Chiang (Created page with '='''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-qua…')
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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.

Results