---
name: "contig_to_chr_coords"
section: "1"
platform: "linux"
package: "tophat"
version: "2.1.1+dfsg1-2+b1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/contig_to_chr_coords"
---

# contig\_to\_chr\_coords(1)

tophat component taking NCBI seq\_contig file and maps contig coords

## NAME

contig\_to\_chr\_coords - tophat component taking NCBI seq\_contig file and maps contig coords

## DESCRIPTION

contig\_to\_chr\_coords: Takes the NCBI seq\_contig file and maps contig coords to whole chromosome coords in a GTF, GFF, or BED file

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  contig\_to\_chr\_coords.py \<format\_flag\> \<seq\_contig.md\> \<junctions.bed\|transcripts.gff\|transcripts.gtf\>

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  for help use **--help**