How to extract fasta sequences from assembled transcripts generated by Stringtie
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4.4 years ago
seta ★ 1.5k

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

stringtie gtf file fasta sequences • 5.9k views
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use gffread, you can find it in cufflink package

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4.0 years ago
zzqr ▴ 50

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.

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2.0 years ago
Juke34 ★ 6.3k

I use agat_sp_extract_sequences.pl from AGAT.

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

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4.0 years ago

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


UPDATE

Here is the perfect solution

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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

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

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7 months ago
DNAvinci • 0

Per, http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread_ex

gffread \
-w assembled_transcripts.fa \
-g ref_genome.fa \
-E cov_refs.gtf \
./stringtie_output.gtf
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