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alekseyzimin / EviAnn_release

This is the standalone version of the EviAnn pipeline
GNU General Public License v3.0
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RNA-Seq data in liftover mode #5

Open asan-emirsaleh opened 4 months ago

asan-emirsaleh commented 4 months ago

Hello! I recently tried EviAnn in liftover mode following your example:

/path/EviAnn-X.X.X/bin/eviann.sh -t 24 -g /path/genome.fasta -e $PWD/transcripts.fa -r $PWD/proteins.faa -l

But there is a note in the usage parameters description:

-r AND one or more of the -p -u or -e must be supplied.

Passing protein sequences without read data causes an error.

Best regards Asan

alekseyzimin commented 4 months ago

What it the error you are getting?

asan-emirsaleh commented 4 months ago

The difference was that I had omitted -e parameter because of the cds were totally duplicated protein accessions in nucleotide dimension. The error was:

Must specify at least one non-empty file with filenames of RNAseq reads with -p or -u or a file with ESTs from the same or closely related species with -e

Now I will try with supplying cds sequences. Best regards Asan

alekseyzimin commented 4 months ago

Yes, you have to specify both transcripts and proteins.

On Thu, Mar 14, 2024 at 9:30 PM Asan Emirsaleh @.***> wrote:

The difference was that I had omitted -e parameter because of the cds were totally duplicated protein accessions in nucleotide dimension. The error was:

Must specify at least one non-empty file with filenames of RNAseq reads with -p or -u or a file with ESTs from the same or closely related species with -e

Now I will try with supplying cds sequences. Best regards Asan

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