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Question: sum all but first 500 lines
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gravatar for Brad Langhorst
4.6 years ago by
Brad Langhorst • 100
United States
Brad Langhorst • 100 wrote:

I'd like to make a genome coverage distribution plot using the X-Y plotting tool

X = coverage depth

Y = fraction of reads at coverage depth.

I'd like to sum up all the coverage beyond 500X and consider that 500X+ to avoid a very wide X axis.

I can cut off the first 500 lines in galaxy, but I don't see how to retain the remaining lines for me to operate on.

Any ideas?

I could do this with a little script, but I'm wondering about how to do this with the galaxy native tools.

 

 

 
galaxy • 845 views
ADD COMMENT • link •
modified 4.6 years ago by Bjoern Gruening ♦ 5.1k • written 4.6 years ago by Brad Langhorst • 100

Nice! Thanks for sharing!

ADD REPLY • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k
1
gravatar for Bjoern Gruening
4.6 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Brad,

the tool "Remove beginning of a file" can remove the first 500 lines for you. Is that what you are searching?

Cheers,

Bjoern
ADD COMMENT • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k
1

Perfect!

I've published the workflow in case anyone has a similar itch.

ADD REPLY • link written 4.6 years ago by Brad Langhorst • 100
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