Hi
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
abc_F3.csfasta
abc_R5-BC.csfasta
abc_F3_QV.qual
abc_R5-BC_QV.qual
thanks !
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
abc_F3.csfasta
abc_R5-BC.csfasta
abc_F3_QV.qual
abc_R5-BC_QV.qual
thanks !
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