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.
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 )
pierre.peterlongo Thank you. I tried BLAT but could got the following error. Any suggestion on what may have caused this.
blat genome.fasta transcripts.fasta -out=psl ouput.psl
Line too long (more than 536870912 chars) line 2 of genome.fasta
1) wrong user id. I'm not P Peterlongo
2) show us the output of
head -n 2 genome.fasta | cut -c 1-500
Thanks Pierre Lindenbaum :)
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?
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