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-   -   Transcriptome Generation -Salmon (http://seqanswers.com/forums/showthread.php?t=87789)

NDUFB11 02-20-2019 05:39 AM

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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