How to sort Grch37 gtf file ?

rrazaghi / modbamtools

Set of tools to manipulate and visualize modified base bam files

Apache License 2.0

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How to sort Grch37 gtf file ? #19

Closed xiucz closed 1 year ago

xiucz commented 2 years ago

Hi, Thank your for your tool, when I test it on my hg19 bam file , but I find the downloaded data gtf file is based on 38. How to prepare to sort the https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh37_mapping/gencode.v42lift37.annotation.gtf.gz file ?

Best, xiucz

yusmiatiliau commented 1 year ago

Hi, I recently sort a gtf file using gff3sort that seems to work with modbamtools: gff3sort.pl --precise /path/file.gtf > /path/filesorted.gtf then bgzip and tabix: bgzip -c /path/filesorted.gtf > /path/filesorted.gtf.gz tabix -p gff /path/filesorted.gtf.gz

I installed gff3sort via bioconda: https://anaconda.org/bioconda/gff3sort

hope it helps