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gaoyubang / nanom6A

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about parameter #10

Open xj-Liang-Olga opened 3 years ago

xj-Liang-Olga commented 3 years ago

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 commented 3 years ago

You can convet it from gff file image

xj-Liang-Olga commented 3 years ago

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 commented 3 years ago

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