Hi Authors,
I have tried to post-process the example-output with "run_blast_os_par.py" but failed. Any advice? I see that the original paper is now online on Nature Comms so I hope there will be more post-processing scripts avail to the users.
Btw, I tried to read the code within "align_extract_reads_script.sh" and understood that it is trying take an aligned BAM from RNA-seq aligner as input and then realign the unmapped again onto the reference genome (WGS) using bowtie2. Wouldn't this weed out some HERVs which we intend to find with virnatrap in the first place? Additionally, there are hERVs included in the reference transcriptome of some RNA-seq analysis pipelines and would render some viral reads, as mapped, and won't be curated for the subsequent virnatrap's assembly anymore. Am I overthinking or we need to be tweaking those preprocessing scripts further? Thanks!
-JQ Lim
Hi Authors,
I have tried to post-process the example-output with "run_blast_os_par.py" but failed. Any advice? I see that the original paper is now online on Nature Comms so I hope there will be more post-processing scripts avail to the users.
Btw, I tried to read the code within "align_extract_reads_script.sh" and understood that it is trying take an aligned BAM from RNA-seq aligner as input and then realign the unmapped again onto the reference genome (WGS) using bowtie2. Wouldn't this weed out some HERVs which we intend to find with virnatrap in the first place? Additionally, there are hERVs included in the reference transcriptome of some RNA-seq analysis pipelines and would render some viral reads, as mapped, and won't be curated for the subsequent virnatrap's assembly anymore. Am I overthinking or we need to be tweaking those preprocessing scripts further? Thanks!
-JQ Lim