From 206623ad9de531e1e96e1d3655f1df9886c05b9e Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Wed, 17 Apr 2024 14:19:34 +0200 Subject: [PATCH] Update agat_convert_minimap2_bam2gff.md --- docs/tools/agat_convert_minimap2_bam2gff.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/tools/agat_convert_minimap2_bam2gff.md b/docs/tools/agat_convert_minimap2_bam2gff.md index 6bf437d1..46e2d388 100644 --- a/docs/tools/agat_convert_minimap2_bam2gff.md +++ b/docs/tools/agat_convert_minimap2_bam2gff.md @@ -2,9 +2,11 @@ ## DESCRIPTION -The script converts output from minimap2 (bam or sam) into gff file. -To get bam from minimap2 use the following command: -minimap2 -ax splice:hq genome.fa Asecodes\_parviclava.nucest.fa | samtools sort -O BAM -o output.bam +The script converts output from minimap2 (bam or sam) into GFF file. +To get bam from minimap2 use the following command: + +minimap2 -ax splice:hq genome.fa Asecodes\_parviclava.nucest.fa | samtools sort -O BAM -o output.bam + To use bam with this script you will need samtools in your path. ## SYNOPSIS @@ -17,8 +19,6 @@ agat_convert_minimap2_bam2gff.pl --help ## OPTIONS -if ( !GetOptions( 'i|input=s' => \\$opt\_in, - - **-i** or **--input** Input file in sam (.sam extension) or bam (.bam extension) format.