How to Annotate Gene names in *.bedmethyl files generated from ModKit?
I have few *.bedmethyl.gz files generated from modkit pileup command, and I need get the gene names annotated for further analysis.
I tried bedtools intersect -a /path/to/all_samples_HP1_merged.bedmethyl.gz -b genomic.gtf -wa -wb but got a warning:
***** WARNING: File /path/to/all_samples_HP1_merged.bedmethyl.gz has inconsistent naming convention for record:
chr1 10468 10469 a 1 . 10468 10469 255,0,0 1 0.00 0 1 00 0 0 0
Is there any other way to do it effectively?
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Vaishnav •
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Can you check if the issue mentioned in here (https://github.com/arq5x/bedtools2/issues/628 ) is applicable in your case?
Hey mate, no this is relevant to my question. I am trying to solve the error alone, I'll post the answer if I solve it.
So to confirm, the chromosomes names match in your GTF and bedmethyl files and you are still getting the warning?
No they didn't match, so I changed it using
chromToUcsc.