This is a test version of Biostars. For the public version, visit https://www.biostars.org.
GFF3 to fasta (error)

Hi im trying to extract some sequences from my GFF3 file to fasta but when I run this:

$   bedtools getfasta -fi Muschr4.fsa -bed Muschr4.fsa.mod.pass.list.gff3 -fo ERVCom.fa

I get

WARNING. chromosome (seq0) was not found in the FASTA file. Skipping.
WARNING. chromosome (seq0) was not found in the FASTA file. Skipping.
WARNING. chromosome (seq0) was not found in the FASTA file. Skipping.
WARNING. chromosome (seq0) was not found in the FASTA file. Skipping.
gff3 fasta
• 2,108 views • link
updated by Ram Ram • written by wocana • wocana

Do chromosome identifiers match in fasta and GFF files? That is the first thing to check. These are warnings so they may be benign.

• 1 views • link
written by GenoMax GenoMax

Paste the output of these commands here

grep ">" Muschr4.fsa | head -10

AND

grep ">" Muschr4.fsa | grep "seq0"
• 1 views • link
written by lakhujanivijay lakhujanivijay 
intirules@Biointi:~/Desktop/Tesis/Secuencias/PruebaRetriever$ grep ">" Muschr4.fsa | head -10

>NC_000070.6 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J

intirules@Biointi:~/Desktop/Tesis/Secuencias/PruebaRetriever$ grep ">" Muschr4.fsa | grep "seq0"

intirules@Biointi:~/Desktop/Tesis/Secuencias/PruebaRetriever$

Then i tried with bed but still no working

• 1 views • link
updated by GenoMax GenoMax • written by wocana • wocana

It looks like you have things named seq0 in your GFF file but not in fasta file. Can you confirm by grep "seq0" your_gff | head -5

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

• 1 views • link
written by GenoMax GenoMax

1 answer 

awk '{if ($1~/[0-9]+/) print $10"\t"$1}' Muschr4.fsa.mod.pass.list > Muschr4.fsa.mod.pass.list.extract
perl $path/LTR_retriever/bin/call_seq_by_list.pl Muschr4.fsa.mod.pass.list.extract -C Muschr4.fsa.mod > Muschr4.fsa.mod.pass.list.extract.fa

This solved it

• 1 views • link
updated by GenoMax GenoMax • written by wocana • wocana

Log in to answer this question.

More posts like this