Split the Gff file based on the strand information

Question

[wu.zhiqiang.1020]

Dear all,

I have a small question to ask:

How can I split the gff file into two separate files based on the strand information (+/-): the strand information is the 7th column. I hope to get two independent files for forward and reverse gff.

Is there any script that could help?

thanks ZQ

How can I just based on the 7th column to extract the gff file?

for example: if 7th matched with "+", then it will be Forward gff;

if 7th matched with "-", then it will be as reverse gff

any idea how to extract?

thanks

[GenoMax]

Have you tried a simple grep + and grep -v + filename ?

[wu.zhiqiang.1020]

thanks your point. but it can not give you complete result. for example as in second line:

NC_024218.1 Gnomon CDS 8938650 8939467 . + 2 ID=cds98;Parent=rna107;Dbxref=GeneID:101952514,Genbank:XP_008166494.1;Name=XP_008166494.1;gbkey=CDS;gene=TMTC3;product=transmembrane and TPR repeat-containing protein 3 isoform X2;protein_id=XP_008166494.1

NC_024218.1 Gnomon mRNA 9963121 10072488 . - . ID=rna123;Parent=gene61;Dbxref=GeneID:101932175,Genbank:XM_005279137.2;Name=XM_005279137.2;gbkey=mRNA;gene=ATP2B1;model_evidence=Supporting evidence includes similarity to: 22 Proteins%2C and 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 8 samples with support for all annotated introns;product=ATPase%2C Ca++ transporting%2C plasma membrane 1%2C transcript variant X1;transcript_id=XM_005279137.2

in some gene annotation, they have the "+" in gene ID column, and it will also report.

thanks

Answer 1

[Alex Reynolds]

$ gff2bed < input.gff | awk '$6=="+"' > output.forward.bed
$ gff2bed < input.gff | awk '$6=="-"' > output.reverse.bed

[wu.zhiqiang.1020]

thanks for the late reply. it is good. ZQ