about parameter

[xj-Liang-Olga]

Hello, when I predict the m6A site, I see the -r parameter which is the file of referance corrd of transcripts. I want to know how to obtain this file and whether it can be converted from a gff file.

[gaoyubang]

You can convet it from gff file

[xj-Liang-Olga]

Hello, I have obtained the bed file with your help, and I would like to ask about the parameters of samtools. I did not find the parameter R, may I ask how to set it.
`$samtools dict

About: Create a sequence dictionary file from a fasta file
Usage: samtools dict [options] <file.fa|file.fa.gz>

Options: -a, --assembly STR assembly
-H, --no-header do not print @hd line
-o, --output STR file to write out dict file [stdout]
-s, --species STR species
-u, --uri STR URI [file:///abs/path/to/file.fa]
`

[gaoyubang]

you need picard to create ref.dict
picard CreateSequenceDictionary R=ref.fa O=ref.dict