You could also convert your reads to fasta format (use reformat.sh from BBMap) and then use blat for the alignments.
Once you identify the reads that align I suppose you want to do a multiple sequence alignment?
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Run bbmap.sh on its own to see all the command line options.
Here are some relevant options
Post-Filtering Parameters:
idfilter=0 Independant of minid; sets exact minimum identity
allowed for alignments to be printed. Range 0 to 1.
subfilter=-1 Ban alignments with more than this many substitutions.
insfilter=-1 Ban alignments with more than this many insertions.
delfilter=-1 Ban alignments with more than this many deletions.
indelfilter=-1 Ban alignments with more than this many indels.
editfilter=-1 Ban alignments with more than this many edits.
inslenfilter=-1 Ban alignments with an insertion longer than this.
dellenfilter=-1 Ban alignments with a deletion longer than this.Last edited by GenoMax; 05-01-2015, 10:37 AM.Leave a comment:
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BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.
Added: Is your reference 200 bp long?Leave a comment:
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Comparing Merged Seqs to a Reference Seq
Hello,
I recently received paired-end reads from an amplicon library I sequenced with Illumina. I used BBMerge to merge the paired-ends and, now, I would like to compare my merged sequences to a reference. My goal is to analyze where the merged sequence may differ from the reference.
I have tried to write a small Perl program, but I am continually running into problems. I study DNA repair and, essentially, I would like to compare my merged sequences to the reference so that I may better understand repair efficiency.
Is anyone aware of any programs/scripts that could help me reach my goal of comparing my merges to a reference? They are about 200bp long. Thank you!
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