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Question: BAM tool?? tab-delimited, coordinate sorted output file - displays calls, depth at every coordinate?
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gravatar for zhalford
3 months ago by
zhalford • 0
zhalford • 0 wrote:

I'm trying to figure out how to create a tab-delimited, coordinate sorted, file type that displays the depth at each coordinate included in the .bed file.

What file can I start with and what tools, if possible, can I use to modify to get the intended result I need?
samtools bam • 145 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by zhalford • 0
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Is your input BAM or BED? If BED, try the tools in the tool group BEDTools.

Variant calling and other analysis workflows are covered in the Galaxy tutorials: https://galaxyproject.org/learn/

FAQs: https://galaxyproject.org/support/ >> Common datatypes explained

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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