This is a test version of Biostars. For the public version, visit https://www.biostars.org.
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"
rna-seq blast blastx hisat2 featurecounts

1 answer

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

gffread is a different program and is part of stringtie package.
gff2fasta.pl seems to come in two versions: one and two separate repos.

Thank you Fatima, gffread works well for that.

Log in to answer this question.