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Old 09-01-2011, 12:07 PM   #1
Junior Member
Location: Cambridge

Join Date: Jan 2011
Posts: 7
Default BWA parameters for mRNA-seq aligning against mRNA refseq


I am sure similar questions were posted earlier but I could not find the definitive answer.

So the question is what parameeters would you use for mapping 1/16 chip data from single-cell mRNA-seq against mRNA refseq database. I am mostly interested in diferential expression of genes not SNPs, gene fusions, etc.

I used bwa with standard parameters "bwa aln -c -t 4 ..." and I have got extremely low mapping yield e.g. from total 40 291 303 reads, 8 529 466 reads were mapped to 6541 refseqs (of more than 36 000 refseqs in the data base).

Any idea how to obtain better mapping?


kwicher is offline   Reply With Quote
Old 09-19-2011, 04:45 AM   #2
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Location: Germany

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What yields do you get mapping to the whole (human ?) genome, then counting reads after the mapping step ? The EdgeR package was quite good for this purpose for me and has a nice tutorial available online.

I think mapping rates of 50% are quite normal for Solid data, and in my human transcriptomes it seems about 30-50% may be mapping outside exons (Illumina data). I've not looked at this in detail so far though.
colindaven is offline   Reply With Quote

alignment, bwa, mrna-seq, parameters, solid

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