Question: GFF3 to fasta (error)
0
gravatar for wocana
9 months ago by
wocana10
wocana10 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 • 290 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by wocana10
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 9 months ago by genomax64k
1

Paste the output of these commands here

grep ">" Muschr4.fsa | head -10

AND

grep ">" Muschr4.fsa | grep "seq0"
ADD REPLYlink modified 9 months ago • written 9 months ago by bioExplorer3.7k
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 9 months ago by genomax64k • written 9 months ago by wocana10
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 9 months ago • written 9 months ago by genomax64k
0
gravatar for wocana
9 months ago by
wocana10
wocana10 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 9 months ago by genomax64k • written 9 months ago by wocana10
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