Multi-fasta file for gffread
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
GTF file generated by stringtie merge has two source ensemble and stringtie
written by musk •
-
How to get human cDNA sequences together with UTR regions?
written by Apex92 •
-
confusion about gffread extracting transcript sequence based on stringtie merge gtf
written by liyong •
-
Extract transcript fasta sequences using gtf
written by otieno43 •
-
StringTie merged transcripts for two different conditions
written by vitor •
-
Extract transcript fasta using gff
written by boczniak767
-
free(): invalid next size (normal) Aborted (core dumped)
written by Mithil Gaikwad •
-
cufflinks transcripts to ensemble or NCBI transcript
written by Tania
-
Could not find fasta record: CuffCompare & Cuffmerge
written by EpiExplorer
-
error in cuffmerge
written by zizigolu
You need to provide genome file as input along with the GTF.
specifically this:
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
CDNFASTQfiles from ENSEMBL ... that does not seem right. Do you meanFASTAfile? Those files are not suited to extract transcripts with gffread. Make sure to study what the tools do.