Hello
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?
Thanks
K.
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?
Thanks
K.
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