User: saygingulec

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Posts by saygingulec

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Comment: C: How can I add sequences to my BED file?
... I tried that but I get this error: [W::fai_get_val] Reference I 11140 11240 not found in FASTA file, returning empty sequence [faidx] Failed to fetch sequence in I 11140 11240 P.S. Chromosome names in my file look like "I" instead of "chrI". I fixed the fasta files for that. ...
written 3 months ago by saygingulec0
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Comment: C: How can I add sequences to my BED file?
... The input looks like this: chrI 11140 11240 1 NM_058259.4 + chrI 11240 11340 2 NM_058259.4 + chrI 11340 11440 3 NM_058259.4 + chrI 11440 11540 4 NM_058259.4 + chrI 11540 11640 5 NM_05 ...
written 3 months ago by saygingulec0
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How can I add sequences to my BED file?
... I have a text file formatted like BED and I want to add the sequences as a column on to it. Bedtools getfasta should be doing that with -bedOut option but as explained in this post (https://github.com/arq5x/bedtools2/issues/571), it doesn't work as it is supposed to. I also tried to download the seq ...
bedtools bed written 3 months ago by saygingulec0

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