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Old 04-30-2013, 09:15 AM   #1
Location: Brazil

Join Date: Apr 2013
Posts: 17
Default Need help with blast...

Does anyone know if I need to make a assembly of my alignment before attempting to make a blast?
I'm asking because after I do an alignment on BWA, I created a file in fasta format to make a blast. But the output file is similar to a sequence without anything aligned.

Someone can help me?
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Old 04-30-2013, 09:21 AM   #2
Cofactor Genomics
Registered Vendor
Location: St. Louis

Join Date: Jan 2010
Posts: 52

Hello Guigra,
Can you share your alignment parameters with the group here... as well as confirm you expect the two to align because you established this with the prior BWA alignments? There are a number of very experienced BLAST users on the board here (as well as on our team) that can help if you provide more information.

My best.

Jarret Glasscock
Cofactor Genomics
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Old 04-30-2013, 09:32 AM   #3
Location: Brazil

Join Date: Apr 2013
Posts: 17

After doing the alignment with BWA, I need to pass the generated file to fasta format, so I can make a blast.
But when I do this, apparently the fasta file generated seems only the reads. Lose alignment. You know what's happening?
I use te samtools to pass the file in sam format for bam format, and after I use the blast2fastx to convert the alignment in bam format to fasta format.
I don't know if have some influence, but I'm work with the paired-end.
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Old 05-01-2013, 10:11 AM   #4
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

FastA *is* only the sequence; aka, reads. The alignment and other information will be lost.
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