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

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!

gft gff3 tomato
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updated by igor igor • written by donger1103 • donger1103

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

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written by erwan.scaon erwan.scaon

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

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written by donger1103 • donger1103

1 answer

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

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written by igor igor

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:)

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written by donger1103 • donger1103

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