Filter SOLiD reads for gene of interest then assemble

[john1923]

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

[colindaven]

Hi John,

I would start this way - of course there may be better options

-obtain the sequence of your gene and surrounding regions

-convert to colour space

-align reads against this sequence (bwa, bioscope, bfast etc)

-use perl/grep to get sequences of those reads which aligned.

-filter - with Galaxy, R, or FastX etc

-realign to check for any differences due to filtering (if any)

Good luck
Colin

[john1923]

Thankyou, that was exactly the reply I was looking for.

All of the programs seem to be installed on my department's bioinformatics server. Now I just have to work out how to use them.

Thankyou