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333 results • Page
1 of 7
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Filtering for tag:
IGV
•
reset
0
votes
0
replies
49
views
Visualize in IGV mitochondrial variants found with MToolBox
IGV
MtoolBox
Mitochondria
5 days ago by
BIN
• 0
2
votes
5
replies
392
views
I could not load GTF data at IGV("Could not create index file") Please help me :)
gtf
igvtools
igv
sort
index
updated 5 days ago by
GenoMax
99k • written 6 days ago by
samuel0325
• 0
1
vote
3
replies
576
views
Nanopore structural variant calling - more than 2 alleles on IGV track?
nanopore
structural variant
igv
vcf
updated 11 months ago by
minalj365
• 0 • written 15 months ago by
BioinformaticsLad
▴ 170
2
votes
4
replies
313
views
Visualizing VCF file on IGV
BCFTOOLS
VCF
IGV
updated 12 days ago by
GenoMax
99k • written 12 days ago by
Buffo
★ 1.8k
5
votes
6
replies
416
views
noisy chip-seq peaks
deeptools
macs2
chip-seq
peaks
igv
updated 18 days ago by
jared.andrews07
9.2k • written 19 days ago by
kolikolmakani14
• 0
0
votes
4
replies
242
views
IGV run batch
IGV
19 days ago by
beaferbl
▴ 10
0
votes
1
reply
130
views
[WGS] how to correctly visualize long indels (50nt+)
wgs
indel
visualization
igv
gatk
4 weeks ago by
memento1984_1
• 0
0
votes
0
replies
90
views
How to produce SNP/Indel markers On IGV using differentially expressed genes?
snp
indel
igv
DEG
Markers
5 weeks ago by
mr.ank2999
• 0
0
votes
0
replies
103
views
IGV RNAseq- Splice junction
RNA-Seq
igv
6 weeks ago by
vinishavvenugopal
• 0
0
votes
0
replies
90
views
Horizontal sub-windows for IGV
IGV
bam
6 weeks ago by
German.M.Demidov
★ 2.0k
0
votes
0
replies
73
views
igv track auto scaling fails in batch mode
igv
7 weeks ago by
calvin99
• 0
0
votes
2
replies
89
views
HPV genes visualization on IGV
RNA-Seq
HPV
IGV
alignment
updated 9 weeks ago by
desouzareis.r
▴ 220 • written 9 weeks ago by
amir.saeidian
• 0
0
votes
1
reply
127
views
Comparing ChIP-seq data sets for different mutants
ChIP-Seq
IGV
Normalization
updated 9 weeks ago by
ATpoint
47k • written 9 weeks ago by
Mischa
• 0
3
votes
6
replies
1.6k
views
Error when trying to run IGV on server
igv
updated 9 weeks ago by
kvshamsudheen
▴ 90 • written 19 months ago by
kristina.mahan
▴ 130
1
vote
10
replies
884
views
6 follow
IGV memory on Windows
igv
gff
updated 12 weeks ago by
Noah
▴ 10 • written 11 months ago by
liorglic
▴ 340
0
votes
1
reply
208
views
Genotype SNP with IGV
IGV
NGS
SNP
updated 3 months ago by
Kevin Blighe
72k • written 3 months ago by
biom.andressa
▴ 10
1
vote
1
reply
129
views
How to install IGV on linux mint?
igv
java.xml.bind
3 months ago by
arianc
• 0
4
votes
5
replies
238
views
IGV over SSH?
IGV
SSH
remote
updated 3 months ago by
Pierre Lindenbaum
135k • written 3 months ago by
Richard
▴ 580
14
votes
13
replies
2.1k
views
Tool:
trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
ChIP-Seq
bigwigs
igv
R
visualization
Tool
updated 4 months ago by
Sael
▴ 20 • written 4 months ago by
poisonAlien
★ 3.0k
1
vote
5
replies
329
views
Can I extract annotation file from genbank format or modify on current gff file?
ChIP-Seq
annotation
igv
updated 5 months ago by
Biostar
20 • written 5 months ago by
Ripacoco
▴ 10
1
vote
9
replies
243
views
Difference of transcripts between my GFF file and the IGV results
gff
igv
transcripts
5 months ago by
pablo
▴ 160
0
votes
1
reply
183
views
Is there a way to calculate the IGV coverage base pair size?
IGV
5 months ago by
KIOA
• 0
0
votes
0
replies
192
views
see base quality from IGV
igv
reads
updated 5 months ago by
ATpoint
47k • written 5 months ago by
yliueagle
▴ 230
0
votes
2
replies
421
views
IGV create genome: cytoband not working
IGV
RNA-Seq
updated 5 months ago by
jinkai0621
• 0 • written 18 months ago by
nlehmann
▴ 110
1
vote
2
replies
377
views
Error loading BAM on IGV
software error
igv
bam
updated 6 months ago by
Pierre Lindenbaum
135k • written 6 months ago by
Apex92
▴ 50
0
votes
3
replies
223
views
igv different width on reference gene exon
igv
updated 6 months ago by
Jorge Amigo
12k • written 6 months ago by
Nich
▴ 10
0
votes
2
replies
228
views
VCFs appear inconsistent with view of alignment
vcf
gatk
freebayes
bbmap
igv
6 months ago by
mark.rose
▴ 40
0
votes
1
reply
248
views
Extract number of INDELs of a specific position for bam file or IGV
alignment
ngs
igv
indels
nanopore
7 months ago by
igit_b
• 0
1
vote
2
replies
256
views
Error-prone human genomic sequence data from Illumina sequencing platform
genome
igv
deletions
insertions
updated 8 months ago by
donfreed
★ 1.5k • written 8 months ago by
rbpdee
▴ 40
2
votes
5
replies
537
views
Make genes from GTF annotation searchable in IGV
igv
gtf
gene
8 months ago by
bataloffv
▴ 20
0
votes
2
replies
243
views
genome in IGV session file
igv
session
xml
genome
8 months ago by
mark.rose
▴ 40
6
votes
6
replies
654
views
How to explain that mutations called by Mutect2 are inconsistent with what I saw in iGV?
iGV
GATK
Mutect2
mutation
updated 8 months ago by
davidben
▴ 40 • written 9 months ago by
Makplus T
▴ 70
0
votes
1
reply
2.6k
views
How to prepare a BED file to make a sashimi plot in IGV?
sashimi
BED
IGV
updated 9 months ago by
Juan Felipe Ortiz
• 0 • written 5.3 years ago by
Joseph Hughes
★ 2.9k
1
vote
3
replies
1.8k
views
IGV or IGB
RNA-Seq
IGV
IGB
genome browser
NGS
updated 9 months ago by
xunshengbu
• 0 • written 2.3 years ago by
akivab2
▴ 110
1
vote
6
replies
388
views
Visualizing pacbio-derived alignment in IGV
alignment
igv
bam
pbi
9 months ago by
cugopal
• 0
3
votes
5
replies
599
views
Gene alignment with IGV
igv
alignment
10 months ago by
flappix
▴ 30
4
votes
3
replies
453
views
What could be a reason for peaks called via Macs2 not appearing as real peaks in IGV?
macs2
igv
updated 10 months ago by
ATpoint
47k • written 10 months ago by
Sam
▴ 160
3
votes
4
replies
637
views
Visualizations of chimeric connections in different chromosomes
Assembly
igv
chimeric
junction
inter-chromosomal
updated 10 months ago by
Jim Robinson
▴ 290 • written 17 months ago by
lucas.caue.jacintho
▴ 30
1
vote
7
replies
1.2k
views
IGV Web App inside Flask Server
flask
igv
alignment
bam
updated 10 months ago by
Jim Robinson
▴ 290 • written 22 months ago by
milind_ag
▴ 10
0
votes
0
replies
312
views
IGV NullPointerException problem
alignment
IGV
10 months ago by
life99945
▴ 20
0
votes
0
replies
326
views
How to visualize multiple sequence alignment and read coverage simultaneously
igv
alignment
10 months ago by
callamartyn
▴ 10
0
votes
1
reply
424
views
IGV browser memory leak?
IGV
ram
updated 11 months ago by
JC
12k • written 11 months ago by
alessandro.derzelle
• 0
2
votes
4
replies
384
views
Finding the Refseq Soft-masked Regions
IGV
Refseq
updated 11 months ago by
vkkodali
★ 2.5k • written 12 months ago by
benformatics
★ 2.1k
3
votes
9
replies
447
views
Reads shown in IGV not quantified by featureCounts
RNA-Seq
IGV
featureCounts
11 months ago by
a.palmer
▴ 20
4
votes
8
replies
357
views
visualize my .BAM file in IGV
IGV
.BAM
alignment
bowtie2
RNA
updated 12 months ago by
Pierre Lindenbaum
135k • written 12 months ago by
christiangriffioen
▴ 20
2
votes
3
replies
993
views
IGV error: Error reading BBFile header for bw files
igv
bw
updated 12 months ago by
bhanratt
▴ 40 • written 15 months ago by
weiyanjia2008
▴ 30
0
votes
1
reply
262
views
[IGV] Is it an aneuploidy ?
igv
alignment
sequencing
genome
updated 12 months ago by
d-cameron
★ 2.3k • written 12 months ago by
slfksdjfsdls
• 0
0
votes
7
replies
322
views
Snap aligner to Igv?
snap
igv
aligner
12 months ago by
newbie
• 0
2
votes
3
replies
672
views
Kallisto, --genomebam, and IGV visualization problem
rna-seq
kallisto
IGV
alignment
bam
12 months ago by
jtoker
• 0
13
votes
8
replies
3.6k
views
Trying To Pull Regions From An Online Bam File Without Downloading
samtools
igv
bam
updated 13 months ago by
Nicolas Rosewick
9.3k • written 8.8 years ago by
Wjeck
▴ 480
333 results • Page
1 of 7
Recent Votes
Concatenating fasta files based on prefix ?
Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Bioinformatics startup market analysis
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24k
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Recent Replies
Comment: Bioinformatics startup market analysis
by
gtechbio
▴ 20
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
by
geneticatt
▴ 110
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low).
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★ 2.1k
agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.
Comment: question when using topgo
by
Kevin Blighe
72k
^^ this
Answer: question when using topgo
by
seidel
7.6k
The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
Comment: why my volcano plot looks strange?
by
cpad0112
15k
is it `log10p` or `-log10p` on y-axis?
Answer: How to get GO terms to specific to perticular biological process
by
geneticatt
▴ 110
See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
Comment: How to perform multiple alignment using MAFFT?
by
Dunois
▴ 620
What does your `system()` command look like now, after having added `--anysymbol`? I am guessing you added `--anysymbol` right before that …
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
Are you using this statement in a loop? If so, please refine your command to error out with the file that produces the error - maybe print …
Answer: How to obtain FDR across all regions investigated in DiffBind
by
Rory Stark
★ 1.0k
The "correct" way to retrieve results in `DiffBind` is via the `dba.report()` function. Setting `th=1` returns all results with FDR <= 1.0,…
Comment: Batch effect correction of 2 studies with different covariates
by
Dunois
▴ 620
If you run `RUVseq` on the data from study B only, you'd get predicted values for age and sex but these will be numerical. I suppose you co…
Comment: How to find single copy family from InParanoid output
by
Dunois
▴ 620
I'd just use [`OrthoFinder`][1]. It outputs a separate directory of single copy orthologs if any such (ortho)groups exist in your data set.…
Comment: Concatenating fasta files based on prefix ?
by
seidel
7.6k
Play with the components of the solution @5heikki gave you to troubleshoot and learn. Are you familiar with loops and pipes? The first part…
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