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

Question

[BioinfoBee]

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

Answer 1

[Pierre Lindenbaum]

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 )

[BioinfoBee]

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

[Pierre Lindenbaum]

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

2) show us the output of

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

[pierre.peterlongo]

Thanks Pierre Lindenbaum :)

[BioinfoBee]

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