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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Extract intact Ltrs to fasta #17

Closed intirules closed 6 years ago

intirules commented 6 years ago

Hi, im trying to extract my results from the gff3 file to fasta and i get this

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

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. 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. WARNING. chromosome (seq0) was not found in the FASTA file. Skipping.

Its there another way to get the intact LTRs to fasta ?

oushujun commented 6 years ago

Hello,

Thanks for using LTR_retriever!

You can approach the goal using the following command lines: 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

Please let me know if you need further help.

Best, Shujun

intirules commented 6 years ago

Thx for the rapid response