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Question: Deeptools compute matrix
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gravatar for edward.grow
2.6 years ago by
edward.grow • 10
edward.grow • 10 wrote:

I love Deeptools, and so glad that galaxy has moved them to the main server. It's awesome!

I can get the whole compute matrix/draw heatmap to work with the right input files using hg19 BED/BedGraph.

However, I can't the compute matrix to run with data aligned to cow (bostau7). I know that the http://deeptools.ie-freiburg.mpg.de/ only supported a few genome builds, is this the same case since it migrated to the main server? Any plans in the near future to support a wider array of reference genomes? Or is something else wrong with my workflow?

Thanks!
heatmap galaxy deeptools chip-seq • 916 views
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modified 2.6 years ago • written 2.6 years ago by edward.grow • 10

Can you check that the BED file you are using doesn't have any errors? At least the number of fields appear problematic. Can you post the first line of your BED file?

Regarding reference genomes, usually if you provide your bigwig file and bed file, there is no need for references genomes to be present.

ADD REPLY • link written 2.6 years ago by fidel.ramirez • 0
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gravatar for edward.grow
2.6 years ago by
edward.grow • 10
edward.grow • 10 wrote:

And this is my error report: Fatal error: Exit code 139 () Number of fields in BED file is not standard. Assuming bed3 Found: intervals: 28983 no groups found /galaxy-repl/main/jobdir/012/705/12705672/tool_script.sh: line 9: 25509 Segmentation fault (core dumped) computeMatrix scale-regions --regionsFileName 'group_0.bed' --scoreFileName 'file_0.bw' 'file_1.bw' --outFileName '/galaxy-repl/main/files/015/560/dataset_15560794.dat' --numberOfProcessors "${GALAXY_SLOTS:-4}" --regionBodyLength 500
ADD COMMENT • link written 2.6 years ago by edward.grow • 10
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