Question: How to extract fasta sequences from assembled transcripts generated by Stringtie
3
gravatar for seta
3.7 years ago by
seta1.4k
Sweden
seta1.4k wrote:

Hi all,

I used STAR and stringtie for mapping reads to reference genome and assembly. As you know, the generated assembled transcripts by stringtie are in gtf format. Now, I want to have fasta sequence of assembled transcript. I used gffread, but all sequences had the same header! maybe it's not compatible with stringtie. Could you please help me out to convert assembled transcripts by stringtie in gtf format to fasta format?

Thanks

ADD COMMENTlink modified 16 months ago by Juke344.9k • written 3.7 years ago by seta1.4k

use gffread, you can find it in cufflink package

ADD REPLYlink written 16 months ago by dukecomeback40
2
gravatar for zzqr
3.3 years ago by
zzqr40
zzqr40 wrote:

The stringtie_merged.gtf file have seqname, start, end strand info. So, you can use R GRanges object and getSeq function from GenomicRanges and BSgenome packages to retrive sequences.

ADD COMMENTlink written 3.3 years ago by zzqr40
1
gravatar for lakhujanivijay
3.3 years ago by
lakhujanivijay5.3k
India/Ahmedabad
lakhujanivijay5.3k wrote:

You can also use bedtools getfasta to fetch sequences from GTF or BED files.


UPDATE

Here is the perfect solution

ADD COMMENTlink modified 3.2 years ago • written 3.3 years ago by lakhujanivijay5.3k

I used this, but I run into the following error

"Error (GFaSeqGet): subsequence cannot be larger than 465 Error getting subseq for gene1 (465..1503)!"

Did you had any issues using gffread?

Thanks

ADD REPLYlink written 2.3 years ago by spriyar10

There is a Python script that fixes this error, you can follow A: gffread error when extracting transcript sequences from gtf, coordinates exceed

ADD REPLYlink written 4 months ago by Cristina Zamora0
1
gravatar for Juke34
16 months ago by
Juke344.9k
Sweden
Juke344.9k wrote:

I use agat_sp_extract_sequences.pl from AGAT.

agat_sp_extract_sequences.pl --cdna --gff input.gtf --fasta genome.fa -o output.fa

ADD COMMENTlink modified 13 months ago • written 16 months ago by Juke344.9k
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