Latest
News
Jobs
Tutorials
Forum
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
50 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
Showing top results for tag:
Bedgraph
•
reset
3
votes
4
replies
146
views
Convert per base bedgraph to Bed format
Bedgraph
perbase
Bed
Bedtools
updated 7 days ago by
Alex Reynolds
32k • written 7 days ago by
bioyas
• 0
1
vote
7
replies
259
views
How to merge and average BedGraph files
bedtools
terminal
bg
bedgraph
9 days ago by
a_bis
• 0
0
votes
0
replies
108
views
converting bedgraph to Bigwig by HOMER
HOMER
bedGraph
BigWig
bioinformatics
ChIP-seq
5 weeks ago by
saha.shagnik
• 0
2
votes
1
reply
103
views
bedGraphToBigWig error : Expecting at least 3 words line 1 of chrom.sizes. got 2
bigwig
bedGraph
updated 6 weeks ago by
ATpoint
48k • written 6 weeks ago by
pt.taklifi
▴ 60
2
votes
2
replies
179
views
In methylation sequencing, what does BedGraph value stand for?
bedgraph
methylaion
methylation sequencing
bismark
12 weeks ago by
kwanghoon
▴ 20
0
votes
2
replies
578
views
bedGraphToBigWig: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
bigwig
software error
bedgraph
updated 3 months ago by
Pierre Lindenbaum
135k • written 3 months ago by
hsu
▴ 30
0
votes
3
replies
247
views
How to create a file with annotation track distribution over 1mb bin across a genome
genome
annotation-track
bed
bedgraph
visualization
updated 6 months ago by
Jorge Amigo
12k • written 6 months ago by
dabitz66
• 0
2
votes
4
replies
269
views
bedgraph.sorted or wig to .cov files?
coverage
bedgraph.sorted
bedgraph
wig
updated 9 months ago by
Shalu Jhanwar
▴ 490 • written 9 months ago by
arshkhaira
▴ 10
0
votes
1
reply
199
views
How to use pybedtools bedgraph to bigwig using Ensembl genomes
pybedtools
bigwig.py
ensembl
bedgraph
python2
9 months ago by
frymor2
▴ 10
6
votes
3
replies
280
views
What are these files?
geo
bed
bedgraph
rnaseq
updated 9 months ago by
jared.andrews07
9.3k • written 9 months ago by
ebs15242
▴ 10
0
votes
1
reply
552
views
EPIC methylation manifest GRch38 query
methylation
coordinates
EPIC
bedgraph
CpG
10 months ago by
prasundutta87
▴ 470
1
vote
4
replies
548
views
Calculate correlations between ChipSeq data sets
chipseq
correlation
peaks
bedgraph
macs2
updated 13 months ago by
Rory Stark
★ 1.0k • written 13 months ago by
Assa Yeroslaviz
★ 1.5k
4
votes
7
replies
307
views
sorting for bedtools genomecov doesn't work properly
bedtools
sort
bedpe
RNA-Seq
bedgraph
updated 13 months ago by
Kevin Blighe
72k • written 13 months ago by
Assa Yeroslaviz
★ 1.5k
1
vote
10
replies
845
views
Plotting Bedgraph with multiple chromosome
bedgraph
Sushi
R
14 months ago by
jaqx008
▴ 90
3
votes
2
replies
768
views
variableStep vs fixedStep for range formats
ucsc
formats
bigwig
bedgraph
range
updated 14 months ago by
Biostar
20 • written 2.6 years ago by
m98
▴ 300
3
votes
5
replies
980
views
GEO database - how to use their bedgraph files
RNA-Seq
bedgraph
updated 17 months ago by
Luis Nassar
▴ 420 • written 17 months ago by
Suicyte
▴ 10
1
vote
5
replies
1.4k
views
Obtain ChIPseq peaks from a bedgraph file with continuous regions
ChIP-Seq
peaks calling
HOMER
MACS2
bedGraph
updated 21 months ago by
Biostar
20 • written 23 months ago by
mmaqueda
• 0
0
votes
0
replies
475
views
Overlapping Bedgraph - Microarray ChIP to BigWig for Clustering analysis
Bedgraph
microarray
heatmap
ChIP
bigwig
22 months ago by
Hushus
▴ 20
1
vote
8
replies
4.9k
views
Overlapping regions in a BedGraph file
bedgraph
GRO-Seq
ChIP-Seq
deeptools
updated 22 months ago by
Simply Bioinformatics
▴ 180 • written 5.3 years ago by
Sam
▴ 90
5
votes
4
replies
2.3k
views
Generating a bedgraph from a scored bed file
ChIP-Seq
genome
bedtools
bedgraph
coverage
updated 2.1 years ago by
Biostar
20 • written 6.1 years ago by
Matt Corley
▴ 40
0
votes
3
replies
1.1k
views
Seqmonk: Bedgraph as input ? (EPIC methylation array data)
seqmonk
Bedgraph
methylation
probe design
updated 2.2 years ago by
Charles Warden
8.0k • written 2.3 years ago by
Ankit
▴ 180
2
votes
3
replies
870
views
Transform Bedgraph counts into Gene Counts (DESeq2 input)
Bedgraph
Counts
Gene Counts
updated 2.2 years ago by
gocougs
▴ 20 • written 2.2 years ago by
LuisNagano
▴ 80
4
votes
6
replies
1.7k
views
Visualizing CNV data based from bed or bedgraph format
CNV
IGV
R
bed
bedgraph
2.2 years ago by
sm.hashemin
▴ 90
1
vote
3
replies
745
views
bedgraph file format in IGV: good for observing CNV ?
igv
cnv
bedgraph
2.4 years ago by
Pin.Bioinf
▴ 290
1
vote
2
replies
1.3k
views
Reformating bedGraph files in shell script
bedGraph
bigWig
ucsc
chr
awk
updated 2.4 years ago by
Biostar
20 • written 2.6 years ago by
m98
▴ 300
7
votes
10
replies
2.1k
views
BigWig library for Java
Java
BigWig
BedGraph
updated 2.5 years ago by
holgerbrandl
▴ 30 • written 6.4 years ago by
bow
▴ 790
5
votes
8
replies
1.8k
views
Output bedGraph from genomeCoverageBed is missing "chr"
RNA-Seq
ucsc
genomeCoverageBed
bedGraph
bigWig
updated 2.6 years ago by
Ram
32k • written 2.6 years ago by
m98
▴ 300
7
votes
8
replies
1.4k
views
Stranded RNA-seq data visualization in UCSC
RNA-Seq
stranded
visualization
bedgraph
updated 2.7 years ago by
Rob
4.6k • written 2.7 years ago by
marina.v.yurieva
▴ 550
0
votes
1
reply
1.2k
views
"olambda_treat_afterfiting_all" output file from MACS
MACS
bedgraph
output
updated 2.7 years ago by
Biostar
20 • written 6.4 years ago by
akivab2
▴ 110
0
votes
1
reply
426
views
What should you do if you don't know the wig file is based on GRCH37 or GRCH38?
wig
bedgraph
2.7 years ago by
Shicheng Guo
★ 8.6k
1
vote
8
replies
1.3k
views
bedGraph compress tools
bedtools
bedGraph
2.7 years ago by
marina.v.yurieva
▴ 550
1
vote
5
replies
1.5k
views
How to extrach gene names and peaks from BedGraph or BigWig files
ChIP-Seq
bedgraph
bigwig
peak
updated 3.0 years ago by
Devon Ryan
98k • written 3.0 years ago by
hkarakurt
▴ 110
5
votes
8
replies
4.1k
views
plot a bedgraph
bed
bedgraph
plot
RNA-Seq
3.1 years ago by
sacha
★ 2.1k
0
votes
0
replies
766
views
genome-wide gene occupancy profiles
ChIP-Seq
occupany profile
bedgraph
3.6 years ago by
Assa Yeroslaviz
★ 1.5k
5
votes
6
replies
1.7k
views
How to merge bedGraph records which are next to each other and have the same score?
bedGraph
updated 3.7 years ago by
GouthamAtla
11k • written 3.7 years ago by
James Ashmore
★ 3.1k
2
votes
2
replies
1.5k
views
Effectively search for positions in large bedgraph files using python (or other language if needed)
bedgraph
python
updated 3.7 years ago by
Alex Reynolds
32k • written 3.7 years ago by
DVA
▴ 550
4
votes
3
replies
2.6k
views
Visualising BedGraph files on UCSC [custom tracks]
visualisation
bedgraph
ucsc
genome
updated 3.8 years ago by
Arup Ghosh
2.8k • written 3.8 years ago by
anu014
▴ 180
3
votes
3
replies
5.8k
views
Difference between 'bedgraph' and 'bw' files
bedgraph
bw
updated 4.2 years ago by
igor
12k • written 4.2 years ago by
biotech
▴ 540
0
votes
1
reply
2.4k
views
How to create a bedGraph file for broadPeak peak caller?
broadPeak
bedGraph
ChIP-Seq
peak calling
updated 4.3 years ago by
569497735
• 0 • written 5.2 years ago by
mrs.hope
▴ 10
0
votes
3
replies
1.8k
views
Merge hundreds bedgraph files with unionbedg in one bash line
bedgraph
merge
xargs
bash
4.4 years ago by
Shicheng Guo
★ 8.6k
0
votes
4
replies
2.0k
views
Relationship of bedGraph to wig.
ChIP-Seq
bedGraph
wig
wiggle
updated 4.6 years ago by
Devon Ryan
98k • written 4.6 years ago by
ariel.balter
▴ 140
1
vote
2
replies
1.3k
views
Is there any way to determine whether my sequenced data uses 0- or 1-based coordinates?
sequencing
coordinates
genome
bed
bedgraph
updated 5.0 years ago by
Alex Reynolds
32k • written 5.0 years ago by
biohack92
▴ 150
3
votes
3
replies
1.5k
views
How do I replace a value used in script with a range of values in a file?
Bioinformatics
AWK
bedgraph
updated 5.0 years ago by
tomc
▴ 80 • written 5.0 years ago by
josephmccarter1
▴ 70
0
votes
1
reply
1.2k
views
Two UCSC bedgraph tracks next to each other
UCSC
Custom Track
bedgraph
updated 5.1 years ago by
Chirag Nepal
★ 2.3k • written 5.6 years ago by
kevin.wyatt.mcmahon
• 0
1
vote
4
replies
1.2k
views
Is there a simple way to get the max coverage of a bedgraph file in python?
python
bedgraph
updated 5.1 years ago by
Alex Reynolds
32k • written 5.1 years ago by
rioualen
▴ 480
13
votes
19
replies
3.0k
views
Sum column until a certain value is reached then print that line
awk
bioinformatics
bedgraph
updated 5.1 years ago by
John
13k • written 5.1 years ago by
josephmccarter1
▴ 70
8
votes
7
replies
12k
views
Bed to BedGraph
RNA-Seq
bioinformatics
bed
bedgraph
DaPars
updated 5.2 years ago by
dally
▴ 190 • written 5.2 years ago by
Ati
▴ 30
6
votes
10
replies
2.7k
views
UCSC BedGraph Issue
bedgraph
ucsc
kent
methylation
updated 5.8 years ago by
Maximilian Haeussler
★ 1.4k • written 5.8 years ago by
mbio.kyle
▴ 380
0
votes
0
replies
2.0k
views
GEM mappability > wig/bedgraph : how to interprete
gem
wiggle
bedgraph
mappbility
interpretation
updated 24 days ago by
Ram
32k • written 6.0 years ago by
mehran.karimzade
▴ 180
0
votes
0
replies
1.2k
views
Tool:
tools to get coverage of a particular transcript from bedgraph
bedgraph
tools
Tool
6.2 years ago by
manauwer_raza
• 0
50 results • Page
1 of 1
Recent Votes
Comment: How can I Extract Transposable element from a new genome assembly?
Is the union of cDNA sequences the exome?
Answer: Filter contig fasta file by GC content
Comment: R command worked yesterday, but stalls today?
Answer: R command worked yesterday, but stalls today?
Comment: How to combine 2 incomplete GTF
Answer: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or
Recent Locations •
All
EMBL Heidelberg, Germany,
just now
China,
just now
Vilnius,
1 minute ago
Morocco,
2 minutes ago
France,
2 minutes ago
Belgium,
3 minutes ago
Camden,
3 minutes ago
Recent Awards •
All
Popular Question
to
Farah
▴ 70
Popular Question
to
jaqx008
▴ 90
Popular Question
to
nilus1432
▴ 30
Popular Question
to
sckinta
▴ 610
Popular Question
to
arturo.marin
• 0
Popular Question
to
marongiu.luigi
▴ 560
Teacher
to
JC
12k
Recent Replies
Comment: How to download all the Zn-binding protein sequences from MetalPDB?
by
GenoMax
99k
There is a [flat database available][1] on the site you linked above. It appears to be in XML format so you will need to likely parse that …
Comment: how to select peaks at not transcribed genes
by
ATpoint
48k
Shouldn't you assess transcription by an actual RNA-based assaay such as CAGE or RNA-seq rather than guessing based on PolII?
Comment: R - A bioinformatic analysis programming language for NGS
by
Ram
32k
Sure. I've been meaning to create a how-to on the super/subscript formatting. For super-script, you can use the `<sup> ... </sup>` HTML ele…
Comment: How to run SPAdes assembler with bam files?
by
GenoMax
99k
You should be able to use pipes to string those steps together samtools view -f 12 -F 256 aligned-sorted-deduplicated.bam | samtools s…
Comment: snap installation error
by
Gianluca
• 0
I know this is an old thread but if anyone has the same problem I prefer to write it here because it is one of the first results in google.…
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
That is my concern... this is why I asked in here :)
Comment: how to select peaks at not transcribed genes
by
jared.andrews07
9.3k
In that case, wouldn't you consider all peaks to be associated with transcription? Even if your 232 peaks are not associated with genes, th…
Answer: Filter contig fasta file by GC content
by
GenoMax
99k
Try the following. seqkit fx2tab --name --only-id --gc contigs.fa | awk -F "\t" '{if ($2 < 35) print $1}' | xargs -n 1 sh -c 'seqki…
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
indeed, my IP was for Pol2
Comment: R command worked yesterday, but stalls today?
by
dariober
12k
...besides, [wget](https://www.gnu.org/software/wget/manual/wget.html) has a `-c/--continue` option to resume the download of a partial fil…
Comment: how to select peaks at not transcribed genes
by
jared.andrews07
9.3k
What makes you think genes with a peak are transcribed while those without are not? Unless your IP was for Pol2, this is an overly simplist…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Thank you! I am going to try it :)
Comment: How to combine 2 incomplete GTF
by
GenoMax
99k
Please create a new environment when installing packages. That avoids conflicts. conda create -c bioconda -n agat agat conda acti…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Hi Juke, I am trying to install it and I can't. ![enter image description here][1] [1]: /media/images/bc08978b-10f7-4666-b385-57807b…
Comment: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or
by
cmo
▴ 70
I agree with you, Mensur, that the GTDB is arguably more reliable and comprehensive than NCBI. However, due to the relative greater longevi…
Traffic: 2310 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6