One option in TopHat is --bowtie-n which means you can run it in "-n mode" as described here. The other thing you can change is the -g option:

-g/--max-multihits             <int>       [ default: 20               ]

This value then is used for both the -k and -m options in Bowtie:

-k <int>           report up to <int> good alignments per read (default: 1)
-m <int>           suppress all alignments if > <int> exist (def: no limit)

These two options in TopHat are also passed to different Bowtie steps as the -v or -n mismatches allowed values:

--initial-read-mismatches      <int>       [ default: 2                ]
--segment-mismatches           <int>       [ default: 2                ]

To edit/add options in Bowtie calls in the TopHat python code, look for the function called bowtie() and the following lines in particular:

    bowtie_cmd += [params.bowtie_alignment_option, str(num_mismatches),
                     "-p", str(params.system_params.num_cpus),
                     "-k", str(params.max_hits),
                     "-m", str(params.max_hits),
                     bwt_idx_prefix]

Then add similar lines as the "-k" line there:

e.g., add a line that looks like this:

                     "--seed", "123",

Chris

OK, so I've got TopHat to print the Bowtie command it uses now:

So this is a very basic TopHat command:

python ~/src/tophat-1.1.4/src/tophat.py -p4 /scratch2/easih/refs/hg19/bowtie/hg19 test.fsa

And this is the Bowtie command that is run by TopHat:

bowtie -q --un ./tophat_out/tmp/left_kept_reads_missing.fq --max /dev/null -n 2 -p 4 -k 40 -m 40 /scratch2/easih/refs/hg19/bowtie/hg19 ./tophat_out/tmp/left_kept_reads.fq

Now setting both -m and -g in TopHat leads to these changes:

TopHat:

python ~/src/tophat-1.1.4/src/tophat.py -m1 -g10 -p4 /scratch2/easih/refs/hg19/bowtie/hg19 test.fsa

Bowtie:

bowtie -q --un ./tophat_out/tmp/left_kept_reads_missing.fq --max /dev/null -n 2 -p 4 -k 10 -m 10 /scratch2/easih/refs/hg19/bowtie/hg19 ./tophat_out/tmp/left_kept_reads.fq

So changing -g to 10 in TopHat, changes the values of -k and -m in Bowtie to 10. But setting -m to 1 in Tophat is not passed to Bowtie in this case (-m in TopHat is probably only invoked in Bowtie if you have spliced alignments).

You can always look in the file tophat_out/logs/run.log to see what bowtie command is set.

I think if you want to use Bowtie options like -a, --best, and --strata, you'll have to edit the tophat.py code. One thing is because -g sets both -k and -m, you end up losing control over what TopHat does with the Bowtie command line. So if you just want one alignment for a read that aligns multiple times, you think to set -g to 1 in TopHat, so that Bowtie gets -k1, but if there are two or more alignments for that read it will be rejected by the fact that Bowtie also gets -m1 (reject reads that align more than once).

Chris

thanks so much for this. I am not getting tophat to recognize the -k option. just get the tophat: option -k not recognized are you able to get this to work? thanks again. holly