Question: How Do Tophat Options -G , --Supress-Hits, And Bowtie Options Interplay?
0
gravatar for carmeyeii89
4.8 years ago by
carmeyeii89150
UNAM,MX
carmeyeii89150 wrote:

Hi,

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,

Carmen

-g/--max-multihits <int> [ default: 20 ]
--suppress-hits
-x/--transcriptome-max-hits <int> [ default: 60 ]
ADD COMMENTlink modified 2.4 years ago by cclementddel20 • written 4.8 years ago by carmeyeii89150
0
gravatar for cclementddel
2.4 years ago by
cclementddel20
France
cclementddel20 wrote:

Hello,

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

ADD COMMENTlink written 2.4 years ago by cclementddel20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 937 users visited in the last hour