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TrinityCTAT
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CTAT-VirusIntegrationFinder
BSD 3-Clause "New" or "Revised" License
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How does the summary_report work?
#46
edmundmiller
closed
1 year ago
0
Handling for the scenario where `blastn -query` returns no results
#45
allaway
opened
2 years ago
3
How to confirm the exact integration site for "span" reads
#44
20182531027
opened
2 years ago
1
Nextflow pipeline?
#43
allaway
closed
2 years ago
3
ERROR: could not open genome file /genome_lib/VIF_index_human-plus-hpv16/ref_genome.fa.star.idx//genomeParameters.txt
#42
wangjiaxuan666
closed
2 years ago
1
The latest version can't load the WDL/cromwell-58.jar correctly
#41
wangjiaxuan666
closed
2 years ago
4
fasle positive results caused by RNA alternative splicing
#40
20182531027
opened
2 years ago
1
threshold of this software to detect chimeric reads & distinguish different integration sites
#39
20182531027
opened
2 years ago
4
single reads how tp use
#38
wangjiaxuan666
closed
2 years ago
4
BUG: next index is smaller than previous, EXITING
#37
jianbiaoli
closed
2 years ago
6
SummaryReport: Fixed bed file prefix in WDL, fixes breakpoint in html
#36
brownmp
closed
2 years ago
0
Twophased fp removal
#35
brownmp
closed
2 years ago
0
Twophased fp removal
#34
brownmp
closed
2 years ago
0
Added read filter output option to chimeric_contig_evidence_analyzer.…
#33
brownmp
closed
2 years ago
1
CPU and output directory arguments not being recognized?
#32
parnaljoshi
closed
2 years ago
4
Issue with bamsifter
#31
rpauly
closed
2 years ago
1
RAM requirements listed on installation instructions wiki page?
#30
allaway
closed
2 years ago
3
Added option to call viral snps
#29
joshua-gould
closed
3 years ago
0
Added java. Updated samtools and picard
#28
joshua-gould
closed
3 years ago
0
separate two pass mode for STAR init
#27
joshua-gould
closed
3 years ago
0
updated default memory
#26
joshua-gould
closed
3 years ago
0
Fixed re-use prior STAR.bam
#25
joshua-gould
closed
3 years ago
0
Added flag to disable reports. Added option to run second stage only.…
#24
joshua-gould
closed
3 years ago
0
Increased memory
#23
joshua-gould
closed
3 years ago
0
Option to generate combined host + virus STAR genome as 1st step in the workflow
#22
joshua-gould
closed
3 years ago
0
Added pigz
#21
joshua-gould
closed
3 years ago
0
Made depth plots optional due to memory requirements. Removed unused imports in python code.
#20
joshua-gould
closed
3 years ago
0
Updated Dockerfile. Fixed WDL memory.
#19
joshua-gould
closed
3 years ago
0
add pbzip2. Use r-base to install R
#18
joshua-gould
closed
3 years ago
0
use pbzip2 if tar file is compressed with bz2
#17
joshua-gould
closed
3 years ago
0
Converted to WDL. Added min_reads filter.
#16
joshua-gould
closed
3 years ago
0
Added min reads filter
#15
joshua-gould
closed
3 years ago
0
Jgould
#14
joshua-gould
closed
3 years ago
0
Either take genome lib dir tar file or tgz star reference, gtf, fasta, and fasta index as input
#13
joshua-gould
closed
3 years ago
0
Pass files to tasks instead of genome lib dir
#12
joshua-gould
closed
3 years ago
3
use bedtools to sort gtf
#11
joshua-gould
closed
3 years ago
0
Added comment.char = '', quote = '' to fix:
#10
joshua-gould
closed
3 years ago
0
handle | and spaces in virus
#9
joshua-gould
closed
3 years ago
0
quote chromosome to handle character such as | in chromosome
#8
joshua-gould
closed
3 years ago
0
Display nearest upstream and downstream genes
#7
joshua-gould
closed
3 years ago
0
Include relevant human gene info in the VIF insertion table results
#6
joshua-gould
closed
3 years ago
0
Set report title to output prefix. Removed empty nav bar.
#5
joshua-gould
closed
3 years ago
0
Updated WDL for removing dups, generate index when removing dups
#4
joshua-gould
closed
3 years ago
0
Create final report with IGV and additional images
#3
joshua-gould
closed
3 years ago
0
Added virus IGV report
#2
joshua-gould
closed
3 years ago
1
remove unused argument viral_db_gtf
#1
joshua-gould
closed
3 years ago
1