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Where to get reference fasta transcriptome for Salmon? hyacinth2011 Bioinformatics 1 09-20-2016 09:49 AM

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Old 02-20-2019, 05:39 AM   #1
NDUFB11
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Default 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
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