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Old 01-09-2014, 05:41 AM   #2
Location: Germany

Join Date: Nov 2013
Posts: 20


I hope you would have got the solution for your query,if so can you please share it here as I too got stuck with the same problem.But,the only difference is that I am working with meta-transcriptomics data for which no reference genomes are available.So after assembly I mapped the original read file against the contig file and obtained an output in sam format.

Assemblers used:- SoapDenovo-Trans,Trinity,Metavelvet(didn't worked well with my data)
Mapping tools used :- Bowtie2,segemehl

It will be very helpful if you can post the procedure or steps you have gone through to get the desired information.

Thank you in advance.
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