Hello,
I want use BBmap for estimating transcript expression level from RNA-seq reads. Mapped will be against transcripts, not the genome.
The Manual for BitSeq uses Bowtie with following conditions:
3 mismatches allowed
no 3' trimming (and no 5' trimming) - both default
report reads only if < 100 possible mapping positions
how should the BBmap parameters look like?
is there a parameter for allowed mismatches per read?
will "secondary=TRUE sssr=0.95 maxsites=100" be a good idea for mapping reads to the human transcriptome. sssr=0.95 means approximate how many mismatches per 75 bases reads ~ 2?
should the reads be trimmed and quality filtered before, and if yes with which parameters?
Dietmar
I want use BBmap for estimating transcript expression level from RNA-seq reads. Mapped will be against transcripts, not the genome.
The Manual for BitSeq uses Bowtie with following conditions:
Code:
bowtie -q -v 3 -3 0 -p 4 -a -m 100 --sam
no 3' trimming (and no 5' trimming) - both default
report reads only if < 100 possible mapping positions
how should the BBmap parameters look like?
Code:
bbmap.sh ambiguous=all maxsites2=100 ( secondary=TRUE sssr=0.95 maxsites=100 )
will "secondary=TRUE sssr=0.95 maxsites=100" be a good idea for mapping reads to the human transcriptome. sssr=0.95 means approximate how many mismatches per 75 bases reads ~ 2?
should the reads be trimmed and quality filtered before, and if yes with which parameters?
Dietmar
Comment