Question: Picard tool collect insert size metrics not working
gravatar for jasvinder.kaur
2.8 years ago by
jasvinder.kaur0 wrote:



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.




software error galaxy • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson25k • written 2.8 years ago by jasvinder.kaur0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 Our team is working to correct this through a tool update. Track progress here:

The immediate workaround is to run Picard tools on a local or cloud Galaxy.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k
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