Question

How to generate GFF/GTF file from cDNA transcipts FASTA file?

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19 months ago

BioinfoBee • 0

Hello, Curious to know if its possible to generate gff/gtf file using cDNA transcripts FASTA file. The purpose is to map the gene structural coordinates using the coding cDNA transcripts. Kindly suggest.

Regards, B

gff3 gtf transcript cDNA • 1.4k views

ADD COMMENT • link 18 months ago by BioinfoBee • 0

score 1 · Answer 1 · 2023-03-23

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19 months ago

Pierre Lindenbaum 164k

BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gpertea/gsrc/blob/master/scripts/psl2gff )

ADD COMMENT • link 19 months ago by Pierre Lindenbaum 164k

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pierre.peterlongo Thank you. I tried BLAT but could got the following error. Any suggestion on what may have caused this.

command used: blat genome.fasta transcripts.fasta -out=psl ouput.psl

Error: Line too long (more than 536870912 chars) line 2 of genome.fasta

Regards, B

ADD REPLY • link 18 months ago by BioinfoBee • 0

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1) wrong user id. I'm not P Peterlongo

2) show us the output of

```
head -n 2 genome.fasta | cut -c 1-500
```

ADD REPLY • link 18 months ago by Pierre Lindenbaum 164k

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Thanks Pierre Lindenbaum :)

ADD REPLY • link 18 months ago by pierre.peterlongo ▴ 900

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Pierre Lindenbaum Sorry about that; Here's an output for 2). The input genome looks fine to me, however, its a very large file (>3Gb). Could the error may be related to its size?

>CHR1
TATTATTTTGTGCGAAAAACTACCACTTGTGTCCTAATCCAAGGCAAAAAACTACCAAGTGT
ATAGTTGAAGCTGCACGCTGTATAAACACTCTTTCGGATGGCAAGGCAGCGGTCTGCTGACC
TGCCGACAGTGACGTGCATCTGAAATTCCAAGTGTGCAACATCCCTAGACATGATGCCACGA
TGATACTCTGGAGAATACAGTCGGGCAGCTCCTGCTCGCCCTCGAGCTCGTTCAGGTTACCA
TCGACGGGCCGGCGCCCTTGATGAGTTCCAAGAGCAGCACGCCATAATTGCAGATGTGGCCC
TCGGCTTTCTCCTGGGGTACCAGCCATATACCAATGCATTTCGTTCAGTTGCTACTTTATAA
CTTTTAAAAGTCGAGTATTTAACCAAAAACTACCACATTTCATAGAAACGAAACTATCACTT
GAAAAGTGCCCGATTTACCTCTTCTAAACGCCTTTCTTACGTGTTGGGCCCA

ADD REPLY • link 18 months ago by BioinfoBee • 0