Alignment based on 1 mismatch.

[vishwesh]

Hi
I have a requirement where on aligning reads to reference the mapping is based only on one mismatch with the reference. I need a tool which can map the reads with the reference genome with max of one mismatch. Can some one suggest one.
Thanks in advance.

Regards
Vishwesh

[gringer]

Bowtie2 will do this fine in end-to-end mode. Just set the minimum score to -1 (--score-min C,-1,0) and maximum/minimum mismatch penalties to both -1 (--mp -1,-1).

[vishwesh]

Thanks David Eccles.. Is it possible to do this in bwa aln... if so what parameters should be given...

[gringer]

From the bwa manual it looks like the edit distance option is what you want (-n 1), coupled with zero extensions allowed (-o 0). I have no experience with BWA, so can only do my best to interpret the specifications.

[vishwesh]

Thanks David Eccles.. I am new to bowtie.. the options are bit confusing.. can you please help me the command.. The files I use are not paired ends..

[gringer]

What have you tried? Give me an example, together with the error message, and we'll be better able to solve this problem.

[vishwesh]

I tried this..
bowtie -S all_other_rna -score-min C,-1,0 -mp -1,-1 /home/vishwesh/soft/TLL28_GTAGAG_L004_R1_001_c2.fastaq test.sam

[gringer]

please use bowtie2 for doing this:

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Options for bowtie are quite different from bowtie2.

[vishwesh]

I tried using bowtie2..
here is the error i get..

Error: Encountered internal Bowtie 2 exception (#1)
Command: /data/apps/bowtie2-2.1.0/bin/bowtie2-align --wrapper basic-0 -S all_other_rna -score-min C,-1,0 -mp /home/vishwesh/soft/TLL28_GTAGAG_L004_R1_001_c2.fastaq test.sam
bowtie2-align exited with value 1

command is
bowtie2 -S all_other_rna -score-min C,-1,0 -mp -1,-1 /home/vishwesh/soft/TLL28_GTAGAG_L004_R1_001_c2.fastaq test.sam

let me know if anything is wrong in this command..

[gringer]

your bowtie2 command should look something like this:

bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} -S [<hit>]

[taken verbatim from the manual]

It looks like you haven't specified an index file on the command line, or the index is attached to the wrong arguments. Perhaps something like this would work better (assuming all_other_rna is your bowtie2 index generated with bowtie2-build):

bowtie2 --score-min C,-1,0 --mp -1,-1 -x all_other_rna -S /home/vishwesh/soft/TLL28_GTAGAG_L004_R1_001_c2.fastaq > test.sam