Question: How to set Trinity parameter:--jaccard_clip
0
gravatar for hudiejie
3.6 years ago by
hudiejie20
Singapore
hudiejie20 wrote:

Hi all,

Does any know how to set --jaccard_clip in trinity?

Seems there is no option for this, but for my sample, it is fugal which is needed this parameter:

'If your transcriptome RNA-seq data are derived from a gene-dense compact genome, such as from fungal genomes, where transcripts may often overlap in UTR regions, you can minimize fusion transcripts by leveraging the --jaccard_clip option if you have paired reads. '

trinity • 1.1k views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by hudiejie20
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

To confirm, you are using this version of the Trinity Galaxy tool?
http://toolshed.g2.bx.psu.edu/view/bhaas/trinityrnaseq

If so, then this parameter has not been set as a user-specified option on the tool form. It is a computationally expensive choice and may be why it was originally omitted. Contacting the repository owner through the Tool Shed (log in first) is currently the best way to request an enhancement for a future tool version. The existing version was published over a year ago and there is no information about plans/status for a revision (in Trello).

Another option, if you program, is for you to modify the tool wrapper to add in the option. All Galaxy wrappers in the Tool Shed are open source.

Hopefully one of these alternatives works out for you. Best, Jen, Galaxy team

 

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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