Question: hera_build does not generate index
0
gravatar for OneBiologist
22 months ago by
OneBiologist0 wrote:

Hello there,

I would like to test hera (https://github.com/bioturing/hera) for RNA-Seq analysis including virus-host fusion transcripts. Therefore I need to generate a new index. When I try to do this, I end up without error message but also with empty index files:

$ hera_build --fasta /path/to/hg38_w_vector.fa --gtf /path/to/hg38_ucsc_w_vector.gtf --outdir /path/to/hera_index/ --full_index 1
Scan reference sequence ...
Scan gtf file...
Extract transcript sequence
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact info@bioturing.com if you need further support
Index transcripts in: /path/to/hera_index/transcripts.fasta
Number of sequences     : 0

When I first tried the index building, there was an error because of missing os and os.path, respectively. After adding "import os" to the hera_build script, it ran through without error but as I've shown without correct index. I've tried with and without --grch38 1 with no difference but size of reference.inf (2 vs 25 kb). Hera was installed via miniconda/bioconda without problems. Hera itself seems to run fine. The server uses CentOS Linux release 7.2.1511.

Would be great, if anyone could help me with that.

index rna-seq hera bioconda • 411 views
ADD COMMENTlink written 22 months ago by OneBiologist0

Looks like I had the wrong gtf file for my genome fasta file. I tested with the GRCh38.fa and GRCh38.82.gtf using the link from https://github.com/bioturing/hera and now it seems to work.

ADD REPLYlink written 22 months ago by OneBiologist0
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