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Question: Picard tool collect insert size metrics not working
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gravatar for jasvinder.kaur
2.8 years ago by
jasvinder.kaur • 0
jasvinder.kaur • 0 wrote:

Hi,

 

I am a newbie to RNA Seq analysis and Galaxy. I was trying to calculate the mean inner distance between mate pairs for Tophat2 but when I run the picard tool on the BWA file (paired end files aligned with reference genome), it results in empty files! Not sure what's happening. I tried few different BWA files but all give the same result.

Also, how do I get the information for Std. Dev for Distance between Mate Pairs?

 

I would really appreciate the inputs from experienced users.

 

Thanks,

Jas.
software error galaxy • 1.1k views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by jasvinder.kaur • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is the correct tool to use. There are two issues: 

1. The cluster is problematic right now, so wait until that is clear. We will tweet and/or post something here on Biostars.

2. Many Picard tools have a dependency issue at http://usegalaxy.org. Our team is working to correct this through a tool update. Track progress here: https://github.com/jennaj/support-known-issues/wiki

The immediate workaround is to run Picard tools on a local or cloud Galaxy. https://wiki.galaxyproject.org/BigPicture/Choices

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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