Question: GFF3 to fasta (error)
1
gravatar for wocana
2.1 years ago by
wocana20
wocana20 wrote:

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. Skippin
file extract fasta gff3 • 633 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by wocana20
1

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

ADD REPLYlink written 2.1 years ago by genomax85k
1

Paste the output of these commands here

grep ">" Muschr4.fsa | head -10

AND

grep ">" Muschr4.fsa | grep "seq0"
ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by lakhujanivijay5.1k
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

ADD REPLYlink modified 2.1 years ago by genomax85k • written 2.1 years ago by wocana20
1

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.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax85k
0
gravatar for wocana
2.1 years ago by
wocana20
wocana20 wrote:
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

ADD COMMENTlink modified 2.1 years ago by genomax85k • written 2.1 years ago by wocana20
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