Hi,
I have no experience mapping nextgen sequences back to ref genome, so please excuse my ignorance.
A colleague has generated some SOLID transcriptome sequences and has asked me to map them to the genome. I'm at an undergrad institution, but we have a good server setup that should handle the task.
I've looked through the site here and see people using maq, bowtie ...mapreads.
I'm hoping for help on building an analysis pipeline that will enable us to map the reads, visualize the results on a browser (gff) and get some quantitative dat - % mapped.
Just to see if I could get the reads to amp I took 1 set (cell) and ran mapreads:
mapreads ../xxxx.csfasta references/Chlre4_genomic_scaffolds.fa Q=../xxxxxx_QV.qual I=1 >mapreads.out
I have not tried to quantify the %mapping yet, but estimate 10-20%max.
Any suggestions re: software, parameters, etc appreciated
Charles
I have no experience mapping nextgen sequences back to ref genome, so please excuse my ignorance.
A colleague has generated some SOLID transcriptome sequences and has asked me to map them to the genome. I'm at an undergrad institution, but we have a good server setup that should handle the task.
I've looked through the site here and see people using maq, bowtie ...mapreads.
I'm hoping for help on building an analysis pipeline that will enable us to map the reads, visualize the results on a browser (gff) and get some quantitative dat - % mapped.
Just to see if I could get the reads to amp I took 1 set (cell) and ran mapreads:
mapreads ../xxxx.csfasta references/Chlre4_genomic_scaffolds.fa Q=../xxxxxx_QV.qual I=1 >mapreads.out
I have not tried to quantify the %mapping yet, but estimate 10-20%max.
Any suggestions re: software, parameters, etc appreciated
Charles
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