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Question: Unable to fetch the sequence from human genome using start/stop coordinates
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gravatar for k.panov
8 months ago by
k.panov • 0
k.panov • 0 wrote:

Hello, I am attempting to generate a FASTA from MACS2 generated summits bed file using Galaxy's workflow: "Create MEME-ChIP input FASTA file (500bp centered regions) from MACS2 summits.bed file". This MACS2 bed file was generated from bowtie2 alignment bam file. Homo_sapiens.GRCh38.dna.primary_assembly (downloaded from ensembl) was used as a reference genome. However, when seemingly the same assembly (hg38) was used to fetch sequences I have a following message: 18783 warnings, 1st is: Unable to fetch the sequence from '181351' to '500' for chrom '1'. Skipped 18783 invalid lines, 1st is #1, "1 181351 181851 ag_m_peak_1 30.56049", and nothing was extracted to FASTA. Could you please suggest me any solution? Thanks Konstantin
bed version genome chrom mismatch • 301 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by k.panov • 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,

There is either a 1) problem with the formatting of the Custom genome or there is a 2) chromosome naming mismatch problem between the inputs. Any bed input also needs to be formatted correctly for the datatype specification/chromosome naming.

These topics are covered in the Support FAQs here, including how to submit a bug report for more direct help: https://galaxyproject.org/support/#troubleshooting

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

Thank you! I just found the problem which was (as you suggested) in the differences between chromosome naming in ensembl (just a number) and NCBI (chr+number) All the best Konstantin

ADD REPLY • link written 8 months ago by k.panov • 0

Great! Glad you were able to get this resolved & thanks for letting us know.

ADD REPLY • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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