Transcriptome Generation -Salmon

NDUFB11 · 02-20-2019, 06:39 AM

Hello guys,

I'm analyzing the gene expression profiling in nematode and I want to generate a FASTA file containing the sequence of all the transcripts using Salmon.

It seems that the program can't find a fasta file although I checked and I have in the genome folder named transcripts.fa

It might be that this file contain a sort of error?

Here is the code

Code:

Patrizios-MBP:processing patrizio$ gffread -w genome/transcripts.fa -g genome/ce11.fa annotation/ce11_genes.gtf
Warning: couldn't find fasta record for 'I'!
Warning: getSpliced(NULL,.. ) called!
Warning: couldn't find fasta record for 'I'!
Warning: getSpliced(NULL,.. ) called!
Warning: couldn't find fasta record for 'I'!
Warning: getSpliced(NULL,.. ) called!
Warning: couldn't find fasta record for 'I'!

Thank you

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02-20-2019, 06:39 AM	#1
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	Transcriptome Generation -Salmon Hello guys, I'm analyzing the gene expression profiling in nematode and I want to generate a FASTA file containing the sequence of all the transcripts using Salmon. It seems that the program can't find a fasta file although I checked and I have in the genome folder named transcripts.fa It might be that this file contain a sort of error? Here is the code Code: Patrizios-MBP:processing patrizio$ gffread -w genome/transcripts.fa -g genome/ce11.fa annotation/ce11_genes.gtf Warning: couldn't find fasta record for 'I'! Warning: getSpliced(NULL,.. ) called! Warning: couldn't find fasta record for 'I'! Warning: getSpliced(NULL,.. ) called! Warning: couldn't find fasta record for 'I'! Warning: getSpliced(NULL,.. ) called! Warning: couldn't find fasta record for 'I'! Thank you