This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get GTF file for Rousettus_aegyptiacus?

Hello Biostars, I am working on the genome analysis of Rousettus_aegyptiacus organisms from data obtained ENA database. After the quality checking (Fastqc) of the reads, I have done alignment with hiasat2, index building carried out using the file from NCBI: ftp://ftp.ncbi.nih.gov/genomes/Rousettus_aegyptiacus/CHR_Un/9407_ref_Raegyp2.0_chrUn.fa.gz. Then I tried to check the overall alignment quality score for a few samples, it ranges 92-93%. Now I want to perform stringTie for assembly, In this step, I need the GTF file. I couldn't find it. Please tell me how do I get or generate GTF fie for this organism. Your response highly appreciated! Thank you

stringtie gtf assembly rousettus aegyptiacus
• 3,512 views • link
written by mathavanbioinfo mathavanbioinfo

This is incorrect. Link is about reference (fasta) downloading image. OP is about annotation (GTF/GFF3) file.

• 0 views • link
written by cpad0112 cpad0112

2 answers

You can download the GTF file from NCBI by searching for Rousettus aegyptiacus in the NCBI Assembly portal, select the top hit use the blue Download button as shown in the image below: enter image description here

• 0 views • link
written by vkkodali_ncbi vkkodali_ncbi

It looks like the annotation file and the genomic FASTA files do not have matching genomic seq-ids. If you use the following two files, I expect the seq-ids to be matching:

Genomic FASTA: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/466/805/GCF_001466805.2_Raegyp2.0/GCF_001466805.2_Raegyp2.0_genomic.fna.gz GTF: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/466/805/GCF_001466805.2_Raegyp2.0/GCF_001466805.2_Raegyp2.0_genomic.gtf.gz

You can check which genomic seq-ids were used for the hisat2 index using the hisat2-inspect command.

• 0 views • link
written by vkkodali_ncbi vkkodali_ncbi

Thanks for the response Can you recommend to use gffread package for the convertion of gff to gtf

• 0 views • link
written by mathavanbioinfo mathavanbioinfo

Log in to answer this question.

More posts like this