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 email@example.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.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.