I posted for help in the group, hope someone can help me....Im wondering if I do something wrong in the config file?Thanks
I use the fastq file and bam file from the same person (Im bit confuse in that point if is right)
alignment_file = /media/cri/CRIS_DATA/VIRUSFINDER/FASTQ/02.bam
fastq1 = /media/cri/CRIS_DATA/VIRUSFINDER/seq_1.fastq.gz
mailto = firstname.lastname@example.org
thread_no = 8
detect_integration = yes # if no is provided, VirusFinder will not detect virus integrations
detect_mutation = yes # if no is provided, VirusFinder will not detect viral mutations
The full paths to the following third-party tools are required by VirusFinder:
blastn_bin = /home/cri/Desktop/ncbi-blast-2.5.0+/blastn
bowtie_bin = /media/cri/CRIS_DATA/VIRUSFINDER/bowtie2-2.2.9/bowtie2
bwa_bin = /media/cri/CRIS_DATA/VIRUSFINDER/bwa.kit/bwa
trinity_script = /home/cri/Desktop/trinityrnaseq-2.2.0/Trinity.pl
SVDetect_dir = /media/cri/CRIS_DATA/VIRUSFINDER/SVDetect_r0.8b
Reference files indexed for Bowtie2 and BLAST
bowtie_index_human = /media/cri/CRIS_DATA/VIRUSFINDER/VirusFinder2.0/bw/hg19
blastn_index_human = /media/cri/CRIS_DATA/VIRUSFINDER/VirusFinder2.0/blast/hg19
Parameters of virus integration detection. They are ignored for single-end data
detection_mode = sensitive
flank_region_size = 4000
sensitivity_level = 1
Parameters of virus detection. Smaller min_contig_length, higher sensitivity
min_contig_length = 300
blastn_evalue_thrd = 0.05
similarity_thrd = 0.8
chop_read_length = 25
minIdentity = 80
Dear cristina_sabiers, Hi
I dont think that the VirusFinder is embedded in Trinity assembler software as I have used version 2.2 of it and I did not heard about that and even there is no question in this regard in Trinity group.
So, if you put all the needed programs correctly in your PATH, I suggest that ask your question from Trinity Group which is a very active and strong group.
In addition, maybe this article can helps you. search for the "Configuration file" section, please.
Hope that helps.
Tomorrow I will check once again and reinstall all, if isnt working will post help in the trinity group...Im a newbee so can be I do something wrong.
It is not really a Trinity issue but may be they can help.
I don't see a virus finder in trinity either so am not sure where you are getting that from.
What Trinity package is this?
Is this the test data going through or your own?
I use my own fastq and bam files if is that what you mean :)
I tried with simulation data and results is the same