Question: Absent PDF histogram after running CollectInsertSizeMetrics tool
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deepsubs • 0 wrote:
I am having problems with using the CollectInsertSizeMetrics tool on my NGS bam file. Although it is able to generate the tabular output with the summary statistics (insert sizes and counts etc.), there is no viewable insert size histogram PDF (the data field for that item is returned as 'empty').
Is anyone here able to help me? Happy to share my history and workflow on a one-to-one basis, if necessary.
Many thanks.
Hello, There were and still are some known issues with certain Picard tools. We would like to review your problem and roll it into the other tickets (if tools issue) or help you to work out the proper inputs (if that is the root issue). Are you working at http://usegalaxy.org or can you reproduce the problems there? If so, please send in a bug report and we can review. Click on the bug icon to see the full error and send it in - please include a link your question in the comments section of the form so we can link the two. Thanks for reporting the problem, Jen, Galaxy team
I am working at http://usegalaxy.org. However, there is no bug icon I can find associated with the job item to report it! No error is actually generated when I run the tool....the field appears green, but clicking on it shows 'empty' in the data field, and no pdf file is viewable.
If I share my workflow and history with you, are you able to have a look and see what has gone wrong?
Many thanks.