annotation NA

[lorenzoball]

Hello everyone,

I am trying to use Dekupl to compare RNA expression levels between 2 groups of samples. The first two steps went well (dekupl run and dekupl index) but the dekupl annotate doesn't seem to work even though no error is returned in the logs. More precisely the output resembles to the input DiffCount file from the dekupl run step but then all the annotation columns are full with NAs and the "is mapped" column full with "F" (False). I tried running it several times, emptying the output directory before starting again but it didn't work. I also tried to run again the index using a gff3 file from gencode but nothing changed and I checked I was using the right genome. I m running out of ideas, could anyone help me please ?

[dgautheret]

Hello, DEkupl-annotate hasnt been updated from some time. I would recommend using this instead: https://github.com/Transipedia/Annotate-contigs
Make sure that DEkupl run has completed successfully. It should have produced a table of differential contigs+counts. Use this table as input to Annotate-contigs.

[lorenzoball]

thank yoou very much. The dekupl run output is good.
I tried the tool you indicated me but a weird error has occured. It tells me "Failed to create user namespace" I don't know what this namespace is and how I can create it.
I created a conda envirnoment and installed singularity to run the tool. Here's my config file :
{
"input_file": "/bioinfo/users/lballest/new_annot_tool/merged-diff-counts.tsv.gz",
"sequence_col": "contig",
"id_col": "tag",
"map_to" : ["human"],
"human_fasta" : "/bioinfo/users/lballest/new_annot_tool/hg38.fa.gz",
"human_gff" : "/bioinfo/users/lballest/new_annot_tool/gencode.v37.annotation.gtf.gz",
"output_dir": "/data/kdi_prod/.kdi/project_workspace_0/1438/acl/02.00/Analyse/Newtool_annotB9vsWT",
"keep_col": ["contig","nb-merged-kmer","tag"],
"threads": 10,
"library_type": "stranded"
}

Thank you for your help!