Dear all,
I want to find the SNP in my rice RNA-seq paired-end data, and I try to use bowtie2 to do mapping. My reference is a transcriptome reference.
what type of setting could I use?
To use end-to-end mode or local mode? how to set the report option and score option like --rdg --rfg --score-min ..??
by the way, I know there are small variance between query and reference because they are different subspecies.
Sincerely,
kito
I want to find the SNP in my rice RNA-seq paired-end data, and I try to use bowtie2 to do mapping. My reference is a transcriptome reference.
what type of setting could I use?
To use end-to-end mode or local mode? how to set the report option and score option like --rdg --rfg --score-min ..??
by the way, I know there are small variance between query and reference because they are different subspecies.
Sincerely,
kito
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