Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: tophat multi read alignment
0
gravatar for jaganlakshman
4.6 years ago by
jaganlakshman • 10
United States
jaganlakshman • 10 wrote:

Hi,

How to do --prefilter multi read hits in Galaxy TopHat

Regards

Lakshman
tool tophat • 1.7k views
ADD COMMENT • link •
modified 4.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.6 years ago by jaganlakshman • 10
0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This option is specific to transcriptome-only searches, a feature not yet implemented. However, transcript junctions can be used and the reported hits limited to those locations. Set "Use Own Junctions: Yes" to see the available options. 

In Tophat/Tophat2, an alternate option that may be of interest is '-g/--max-multihits INT' and is named "Maximum number of mismatches that can appear in the anchor region of spliced alignment:" on the tool form. It can be found by setting: "TopHat settings to use: Full Parameter list".

We realize this is not the same operation. If there is an update about the implementation of this search option in the tool, we will update the post.

Best, Jen, Galaxy team
ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

 jaganlakshman Lakshman, After looking into this more, I believe this would be a great enhancment to the Galaxy Tophat2 tool wrapper. I opened a ticket here and credited you for the inspiration, thanks! https://trello.com/c/uVBIwZ6C -Jen

ADD REPLY • link modified 4.6 years ago • written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour