ssrs filtering from gff3 file

Question

[moohit21]

Hello everyone. I have a gff3 file of a genome and a .misa file obtained from misa.pl, is there any script or software present that can extract the ssrs that present on the genic regions of the genome or simply to say how to filter the ssrs present in gff3 file using the coordinates ?

Thank you for the help in advance.

Answer 1

[lakhujanivijay]

You can use bedtools intersect

Here are possible steps:

1. Create a bed file from .misa file

   cut -f1,6,7 your_file.misa > misa.bed

   • Cut the file taking just the columns 1, 6 and 7.
   • col1 is the chr name
   • col6 is the start coordinate of the SSR
   • col7 is the stop coordinate of the SSR

2. Create a gff file with only genic feature entry from your GFF file (of the genome)

   awk -F "\t" '$3=="gene"{print}' > genic.gff

   • cut the GFF file with -F (field separator as <tab>) and match column 3 to feature "gene" and take the whole line

3. Now, use bedtools intersect

   bedtools intersect -a misa.bed -b genic.gff