Question: How to make a custom gtf or gff3 file with a list containing transcript loci
0
gravatar for donger1103
11 months ago by
donger110310
United States
donger110310 wrote:

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 • 455 views
ADD COMMENTlink modified 11 months ago by igor7.6k • written 11 months ago by donger110310

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

ADD REPLYlink written 11 months ago by erwan.scaon670

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

ADD REPLYlink written 11 months ago by donger110310
0
gravatar for igor
11 months ago by
igor7.6k
United States
igor7.6k wrote:

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

ADD COMMENTlink written 11 months ago by igor7.6k

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:)

ADD REPLYlink written 11 months ago by donger110310
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