gffread is a different program and is part of stringtie package.
gff2fasta.pl seems to come in two versions: one and two separate repos.
How to blast my DE genes?
I mapped my transcripts onto the genome using hisat2. Then used featurecounts to generate the expression matrix for DE gene analysis using deseq2. Now I have a list of DE genes and I hope to annotate them using blast+. How do I generate a fasta file for my DE genes so that I can blast them?
The list of DE gene I got is a list of 'Name' of my gff files. My gff:
##gff-version 3
Bany_Scaf21 B_anynana_v2 gene 6190721 6202463 . - . ID=BANY.1.2.t00001.path1;Name=BANY.1.2.t00001
Bany_Scaf21 B_anynana_v2 mRNA 6190721 6202463 . - . ID=BANY.1.2.t00001.mrna1;Name=BANY.1.2.t00001;Parent=BANY.1.2.t00001.path1;coverage=100.0;identity=100.0;matches=1509;mismatches=0;indels=0;unknowns=0
Bany_Scaf21 B_anynana_v2 exon 6202260 6202463 100 - . ID=BANY.1.2.t00001.mrna1.exon1;Name=BANY.1.2.t00001;Parent=BANY.1.2.t00001.mrna1;Target=BANY.1.2.t00001 1 204 +
Bany_Scaf21 B_anynana_v2 exon 6198996 6199148 100 - . ID=BANY.1.2.t00001.mrna1.exon2;Name=BANY.1.2.t00001;Parent=BANY.1.2.t00001.mrna1;Target=BANY.1.2.t00001 205 357 +
Bany_Scaf21 B_anynana_v2 exon 6197487 6197555 100 - . ID=BANY.1.2.t00001.mrna1.exon3;Name=BANY.1.2.t00001;Parent=BANY.1.2.t00001.mrna1;Target=BANY.1.2.t00001 358 426 +
Bany_Scaf21 B_anynana_v2 exon 6197073 6197159 100 - . ID=BANY.1.2.t00001.mrna1.exon4;Name=BANY.1.2.t00001;Parent=BANY.1.2.t00001.mrna1;Target=BANY.1.2.t00001 427 513 +
Bany_Scaf21 B_anynana_v2 exon 6196558 6196686 100 - . ID=BANY.1.2.t00001.mrna1.exon5;Name=BANY.1.2.t00001;Parent=BANY.1.2.t00001.mrna1;Target=BANY.1.2.t00001 514 642 +
My list of DE genes in csv format:
"x"
"BANY.1.2.t20473"
"BANY.1.2.t12787"
"BANY.1.2.t10473"
"BANY.1.2.t10472"
"BANY.1.2.t08098"
"BANY.1.2.t04432"
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I think you can use a gff2fasta converter to get the sequences.
https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html
gffread or gff2fasta.pl
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Thank you Fatima, gffread works well for that.
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