Question: How Do Tophat Options -G , --Supress-Hits, And Bowtie Options Interplay?
gravatar for gaelgarcia05
7.0 years ago by
gaelgarcia05210 wrote:


I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now?

I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments.

Now, the description sounds more like if there are more than g top scoring alignments for a read (assuming report-secondary-alignmennts is not on), it will choose g at random, or simply the top alignments found if they did not reach g. There does not seem to be a discarding of reads if they surpass g. However, there is an option in the help message, not in the manual, that is called --suppress-hits. I suspect this might be able to turn on the discarding of reads that exceed g alignments. Is this true?

And finally, if one sets bowtie options -k and -M (does this still exist?), do those pass on to TopHat, and do they precede over -g?

Thanks a lot,


-g/--max-multihits <int> [ default: 20 ]
-x/--transcriptome-max-hits <int> [ default: 60 ]
ADD COMMENTlink modified 4.6 years ago by cclementddel20 • written 7.0 years ago by gaelgarcia05210
gravatar for cclementddel
4.6 years ago by
cclementddel20 wrote:


I have the same problem I couldn't find any informations about "--supress-hits" option, did you find something ?

ADD COMMENTlink written 4.6 years ago by cclementddel20
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