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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 32k • written 7 days ago by • 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 48k • written 6 weeks ago by ▴ 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 135k • written 3 months ago by ▴ 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 12k • written 6 months ago by • 0
2
votes
4
replies
269
views
bedgraph.sorted or wig to .cov files?
coverage bedgraph.sorted bedgraph wig
updated 9 months ago by ▴ 490 • written 9 months ago by ▴ 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 9.3k • written 9 months ago by ▴ 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 ★ 1.0k • written 13 months ago by ★ 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 72k • written 13 months ago by ★ 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 20 • written 2.6 years ago by ▴ 300
3
votes
5
replies
980
views
GEO database - how to use their bedgraph files
RNA-Seq bedgraph
updated 17 months ago by ▴ 420 • written 17 months ago by ▴ 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 20 • written 23 months ago by • 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 ▴ 180 • written 5.3 years ago by ▴ 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 20 • written 6.1 years ago by ▴ 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 8.0k • written 2.3 years ago by ▴ 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 ▴ 20 • written 2.2 years ago by ▴ 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 20 • written 2.6 years ago by ▴ 300
7
votes
10
replies
2.1k
views
BigWig library for Java
Java BigWig BedGraph
updated 2.5 years ago by ▴ 30 • written 6.4 years ago by ▴ 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 32k • written 2.6 years ago by ▴ 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 4.6k • written 2.7 years ago by ▴ 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 20 • written 6.4 years ago by ▴ 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 98k • written 3.0 years ago by ▴ 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 11k • written 3.7 years ago by ★ 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 32k • written 3.7 years ago by ▴ 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 2.8k • written 3.8 years ago by ▴ 180
3
votes
3
replies
5.8k
views
Difference between 'bedgraph' and 'bw' files
bedgraph bw
updated 4.2 years ago by 12k • written 4.2 years ago by ▴ 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 • 0 • written 5.2 years ago by ▴ 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 98k • written 4.6 years ago by ▴ 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 32k • written 5.0 years ago by ▴ 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 ▴ 80 • written 5.0 years ago by ▴ 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 ★ 2.3k • written 5.6 years ago by • 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 32k • written 5.1 years ago by ▴ 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 13k • written 5.1 years ago by ▴ 70
8
votes
7
replies
12k
views
Bed to BedGraph
RNA-Seq bioinformatics bed bedgraph DaPars
updated 5.2 years ago by ▴ 190 • written 5.2 years ago by ▴ 30
6
votes
10
replies
2.7k
views
UCSC BedGraph Issue
bedgraph ucsc kent methylation
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by ▴ 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 32k • written 6.0 years ago by ▴ 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
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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…
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