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Old 12-07-2011, 10:05 AM   #1
Location: canada

Join Date: May 2010
Posts: 16
Default Please help aligning SOLID PE data

I've been having problem with SOLID pe data and i was hoping you can help. I am use to hiseq data but the tools for SOLID are unclear to me.
I ran my SOLID 50 and 30 bp paired reads with novoalign--that failed; then running with bwa failed because of the way the reads are listed as R5 versus R3 (I forget the exact detail).
I then used BFAST which took forever (2 weeks). then I called mutations with GATK but I only get 5000K variants when I expected over 30K (for agilent sureselect 50M).
Although it is possible the data I have is insufficiently covered, it would be good to know that I have done all the steps properly.

Could you please share your the code that you use to align the csfasta files?
for example, the reads I have have the following naming

thanks !
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Old 12-07-2011, 12:25 PM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 836

The solid reads are aligned in RF orientation (R5-BC for the reverse strand, F3 for the forward strand), so you may need to explicitly indicate this for your alignment programs. I've had trouble aligning with Bowtie paired-end for some reason, but the unpaired reads seem to align fine.
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Old 12-08-2011, 01:20 AM   #3
Location: Sophia-Antipolis

Join Date: Jun 2009
Posts: 10

i use bowtie to align paired-ends reads from SOLiD :
bowtie -f --fr -C -S -I 0 -X 500 --Q1 f3.qual --Q2 f5.qual -1 f3.csfasta -2 f5.csfasta bowtie_index_c algn.sam
Bowtie_index_c must be in color space (bowtie-build -C seq.fa seq_c)
kevleb is offline   Reply With Quote

alignment, paired end, solid

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