Hi,
This is wonderful forum but i wonder why there isn't (at least I cant find) NGS data analysis from A-Z for dummies thread.
Like:
1. If you're using 454, then align reads using XX software and XX reference sequence with settings x y z
example command: samtools mpileup [-EBug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam
2...
3...
Z. And here is your genome sequence with genetic variant annotation and full common qc steps done, ready for case-control (familial, ect.) studies (or whatever you do with it)
Any help with this dream of mine, because I am noob in this NGS thing but have to learn.
Thank you!
This is wonderful forum but i wonder why there isn't (at least I cant find) NGS data analysis from A-Z for dummies thread.
Like:
1. If you're using 454, then align reads using XX software and XX reference sequence with settings x y z
example command: samtools mpileup [-EBug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam
2...
3...
Z. And here is your genome sequence with genetic variant annotation and full common qc steps done, ready for case-control (familial, ect.) studies (or whatever you do with it)
Any help with this dream of mine, because I am noob in this NGS thing but have to learn.
Thank you!
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