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Question: interval file to fastq conversiosn
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gravatar for shapni
9 months ago by
shapni • 0
shapni • 0 wrote:

I want to obtain fastq file from chromosome coordinates. I have interval file which contains 4 columns chromosome number, start and end coordinated and peak numner from chipseq. I have obtained that on mouse mm10. When I use this information in fetch sequences, it generates warning message as invalid chrom, start and end on column values. I am not sure why I am getting this error.

A quick help will be appreciated!

Thanks, Rashmi
fastq dna extract usegalaxy.org fasta • 297 views
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modified 9 months ago • written 9 months ago by shapni • 0

Post a line or two of the interval file.

ADD REPLY • link written 9 months ago by Devon Ryan • 1.9k

chr1 14302133 14302233 R2_POS_narrow_me3_peak_50 chr1 14302729 14302829 R2_POS_narrow_me3_peak_51 chr1 14303573 14303673 R2_POS_narrow_me3_peak_52

Each peak is on the separate line, it may not appear in the display.

Thanks, Rashmi

ADD REPLY • link written 9 months ago by shapni • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Several UCSC genomes, including mm10, will fail with the Extract Genomic DNA tool right now.

We are tracking this in item 2 in the linked ticket below (and for Bedtools getfastabed, which can do a similar operation). A tool update is required to correct the functionality for the first. This is a priority update. The second is already fixed (last week) and is pending an update to Galaxy Main https://usegalaxy.org, please see item 6 in the same ticket.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for shapni
9 months ago by
shapni • 0
shapni • 0 wrote:

Thank you very much for your update!

Rashmi
ADD COMMENT • link written 9 months ago by shapni • 0
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