Question: HISAT2 soft clipping
gravatar for hermane
8 months ago by
hermane0 wrote:

When using default options HISAT2 performs soft clipping. Under scoring options soft clipping is set to NO When scoring options is opened and executed is pressed an error is reported:

tool error An error occurred with this dataset: cannot find 'scoring_options'

When soft clipping is set from default NO to YES the same error is reported.

How can I run HISAT2 without soft clipping?

ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by hermane0
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I can reproduce the problem with the most current tool version at Galaxy Main HISAT2 A fast and sensitive alignment program (Galaxy Version 2.1.0)

Some tests are still running to find out when this was introduced as a problem and if it is server-specific or not. Once completed, I'll comment on this ticket with details:

Thanks for reporting the problem!

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson25k

This has been confirmed to be a problem with the tool wrapper, see latest comments in the ticket.

Test jobs are still executing for the older tool versions - I'd like to be able to give you a workaround. The test history is linked in the ticket.

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour