Comparing Merged Seqs to a Reference Seq

[GenoMax]

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?

[GenoMax]

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.

[lcmb]

BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.

Added: Is your reference 200 bp long?

Yes, it is. Thank you, GenoMax! Will BBMap allow me to set any criteria for the alignment? For example, if I did not want any sequences that differ by more than 10% from my reference.

[GenoMax]

BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.

Added: Is your reference 200 bp long?

[lcmb]

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!