mapping human paired reads to Ecoli

[colonppg]

hi, Folks:

quick question... I have used tophat2 to map to human genome, for some of the samples there are relative low mapped reads.

We suspect there may be too much Ecoli contamination, one suggestion is to map to E coli genome and see % of reads that comes from E Coli.

My questions, can I use tophat2 to do that? The reason is I like the summary log of tophat2... these are paired reads of 50 mers...

thanks in advance...

Thanks
Hao

[Brian Bushnell]

Yes, you can.

[colonppg]

thanks!

thanks for your prompt reply...