ViFi
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namphuon
Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
Hello, I would like to use ViFi with a specific reference file that I have. Therefore, I'm referring to the following content: `#Set up reference for alignment HUMAN_REF="GRCh38" HUMAN_REF_FILE_NAME="hg38full.fa" for...
Hi, I have encountered problems running ViFi on EBV genome with `--disable_hmms`. The possible bug leads to 0 clusters in `output.clusters.txt` and `output.clusters.txt.range` for several samples clearly having traces of...
Hi, I am trying to download the data repository for sSep4 and click the link but it's an empty link. May I have your help to fix it? FYI, the...
I would like to run ViFi with a different reference than the one provided (hg19). I concatenated the reference together with the viral sequence, and indexed it. I provided this...
Hi Nam We were hoping to use ViFi, but it would be useful for organizational purposes if you could version the software. For example, this would be useful for the...
Hi I install docker and execute setup_linux_mac.sh my cmd: sudo python $VIFI_DIR/scripts/run_vifi.py --cpus 2 --hmm_list $VIFI_DIR/data/hbv/hmms/hmms.txt -f $VIFI_DIR/test/data/test_R1.fq.gz -r $VIFI_DIR/test/data/test_R2.fq.gz -o $VIFI_DIR/tmp/docker/ --docke but, I got the following error File...
Hi, We ran ViFi on samples of HCC RNA-seq data downloaded from PRJNA337887 (only one sample test), After manually checking result from ViFi and supplement table 3 of original papers,...
fix samtools reheader which only accept un-compressed sam files as header while pysam version higher than 0.14.
I follow the instructions(install dependencies, set paths, download data and index the reference sequence), and everything's going well. Then I run run_vifi.py using the test data(test_R1.fq.gz and test_R2.fq.gz) and ran...
