How to make a custom gtf or gff3 file with a list containing transcript loci

Question

[donger1103]

Hi everyone, I have a text file containing thousands of tomato transcript loci , such as "SL2.50ch03, 4328007, 4328953" , they are new transcripts. i want to get their transcript sequences as a fasta file. My plan is to make a custom gtf or gff3 file ,then extract the corresponding sequences with gffred tool, therefore, anyone can help me to create a gtf or gff3 file? many thanks!

[erwan.scaon]

Maybe this post can help (in OP comments, there are hints about how to create a custom GTF).

[donger1103]

thanks for your help :-) , i am working on it.

Answer 1

[igor]

It would probably be easier to create a BED file out of them (only the tab-separated coordinates are needed). Then use bedtools getfasta.

[donger1103]

Thanks, it can extract the genomic sequence indeed (i used the genome sequence as input), however, what i need is transcript sequences, are there any other options? Thanks again:)