Multi-fasta file for gffread
0
0
Entering edit mode
12 months ago
Vitor1 ▴ 110

Hey Guys,

I'm having a problem trying to extract the transcripts from a merged StringTie .gtf file with gffread. I have downloaded the cDNA fastq file from ENSEMBL and tried to run the following command:

gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

However I'm getting the following result:

Warning: couldn't find fasta record for '1'! Error: no genomic sequence available (check -g option!).

What should I do in this case? Is this the right fastq file that I have tried?

Thanks

gffread gtf fasta • 651 views
ADD COMMENT
1
Entering edit mode

You need to provide genome file as input along with the GTF.

ADD REPLY
0
Entering edit mode

specifically this:

-g /path/to/genome.fa 

needs to be the actual path to the genome, what you have there is the example from the description.

But for the reference, the command extracts transcripts from a genome, based on transcript information in the GFT file.

You say you downloaded CDN FASTQ files from ENSEMBL ... that does not seem right. Do you mean FASTA file? Those files are not suited to extract transcripts with gffread. Make sure to study what the tools do.

ADD REPLY

Login before adding your answer.

Traffic: 1987 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6