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Old 04-11-2011, 07:22 AM   #1
john1923
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Location: Cambridge

Join Date: Apr 2011
Posts: 7
Default Filter SOLiD reads for gene of interest then assemble

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
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Old 04-12-2011, 12:17 AM   #2
colindaven
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Location: Germany

Join Date: Oct 2008
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Default

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
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Old 04-12-2011, 03:47 AM   #3
john1923
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Default

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
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