How to carryout gene annotation with *.bedmethyl.gz and reference.gtf file ?

[vaishnavpvarma]

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? I wish to analyze Gene Expression levels comparing it to Methylation Patterns and genes associated to it.

[ArtRand]

Hello @vaishnavpvarma,

To be honest I'm not completely familiar with this bedtools warning. Could you give me a link to the GTF you're using (or one that's very similar)? Is your bedmethyl and modBAM a typical whole genome sequencing run aligned to a reference genome? I can see if there is a way to do what you're looking for.