Hi,
There are several SOLiD runs in the Short Read Archive from different haplotypes of the species that I work on.
I want to download this data, extract all of the reads that are homologous to my gene of interest, then analyse and possibly assemble them.
What programs would you use to
-filter the SOLiD reads and extract reads homologus to my gene
-clean any primers/repeats from the sequences
-assemble or analyse the reads.
I have some experience with Linux, Perl and analyzing 454 data. But I am mainly a wet lab biologist.
Thank you in advance.
John
There are several SOLiD runs in the Short Read Archive from different haplotypes of the species that I work on.
I want to download this data, extract all of the reads that are homologous to my gene of interest, then analyse and possibly assemble them.
What programs would you use to
-filter the SOLiD reads and extract reads homologus to my gene
-clean any primers/repeats from the sequences
-assemble or analyse the reads.
I have some experience with Linux, Perl and analyzing 454 data. But I am mainly a wet lab biologist.
Thank you in advance.
John
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