Closed TakashiKoyama closed 6 years ago
Hi,
BLAST_to_BED exclusively works on BLAST-formatted XML files. It looks like rnammer doesn't follow BLAST's XML schema, so it won't work. You can convert your GFF-2, aka GTF, file to a BED file using BEDOPS. Details are found on this Biostars thread.
Hi,
Firstly, I would like to appreciate such a nice tool. I recently run rnammer to identify rRNA loci in my genome. Because my final goal is to mask rRNA loci from bam file for RNA-seq quantification, I need bed file.
rnammer produced either .xml or .gff file but unfortunately gff is version2. I could not find converter from gff2 to bed. So, I decided to convert xml to bed with your script.
Your script did not produce error but output bed was empty. I am not familiar with xml format but I guess my xml might be somehow different from your specification. I attach my xml below. If it’s not too much trouble, could you help me? Thank you for your consideration.