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Question: Bedgraph file problem
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gravatar for jlocker
8 months ago by
jlocker • 0
United States
jlocker • 0 wrote:

I have received a set of BAM files generated from RNAseq (PE100) of the opossum, MonDom5.

When I generate Bedgraph gene coverage files of this data, column 1 lists only a number without the chr designation, i.e., "1" not "chr1". I think this a problem with the BAM files, which do not have the tabular layout of our files from other species. Is there an easy way to fix the BAM files?

Alternatively, is there an easy way to rewrite column 1 in the Bedgraphs?

Thanks
bedgraph chromosome rna-seq bam mismatch • 267 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by jlocker • 0
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Some options for manipulating chromosome identifiers is covered in this support FAQ: https://galaxyproject.org/support/chrom-identifiers/

Also, see the tools listed at the bottom of this support FAQ for common ways to manipulate data within Galaxy: https://galaxyproject.org/support/troubleshoot-an-error/

More tools (including a free-form entry for awk scripts) are in the tool group Text Manipulation.

You could also make the change before loading the data to Galaxy with your own script, a text editor (vi, vim, emacs, etc), or Unix line command utilities (similar in function to many of the Text Mani tools -- and frequently named the same).

All support FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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