Any solid and reliable pipeline for this application?
I would like to use Samtools pile-up and some stat steps, but would like to have the helps for a reliable pipeline established well. Any help is highly appreciated!
P.S. 1) total switch of SNP expression is also interested;
2) have any experience to share for mouse transcriptome?
3) what is the minimal numbers for reads? 30Million or 40Millions?
4) must remove potential PCR duplicates?
Thanks a lot!
I would like to use Samtools pile-up and some stat steps, but would like to have the helps for a reliable pipeline established well. Any help is highly appreciated!
P.S. 1) total switch of SNP expression is also interested;
2) have any experience to share for mouse transcriptome?
3) what is the minimal numbers for reads? 30Million or 40Millions?
4) must remove potential PCR duplicates?
Thanks a lot!
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