Entering edit mode
5.6 years ago
KVC_bioinfo ▴ 570
I am trying to analyze RNA-seq (Human) samples for viral integration. Till now I have come up with few steps for analysis:
1) aligning the RNA-seq data to reference human transcriptome (STAR)
2) separating the unmapped reads/discordant reads
3) aligning the unmapped reads to viral sequence (STAR)
I have done the above 4 steps so far. I am not sure how I should proceed. Also, the alignment of unmapped reads and viral sequence gave me only 0.03% of uniquely mapped reads which is around 1000 reads as per the data I provided.
Can someone help me here for proceeding the analysis. ?
Thank you in advance
Are you looking for a specific virus genome that is expected to be integrated or just contamination of viruses in your data? I would not expect the latter to be an issue with an RNAseq dataset.
I am looking into a specific virus that is expected to be integrated into the samples I have.
See if VirusFinder helps.
Thank you. I looked into this however, I wanted to use latest reference build (38) and that's why I am trying to do analysis on my own and not using existing pipeline
Example shown in the manual is for hg19 but you can substitute any genome you want. See FAQ 6.2 on page 14.
Thank you. I looked into it. seems like it's in pearl script. I am not familiar with it at all. :(
I am trying to do the analysis on my own without using any existing pipeline.
The changes needed are not in the perl script (I only had a quick look at the manual) but in the configuration files of where the genomes indexes as when you run the tool. Read through the manual and see if you are able to figure it out.
I tried. However, I am having trouble with installing SVDetect required in VirusFinder. I have posted the error I got in it in other Biostar post.
meanwhile, I am trying to follow the pipeline VirusFinder has manually. is there any other tool to replace SVDetect?