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Showing top results for tag: chip-seq • reset
0
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25
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how to combined peak score or other quantitative indicator when identify TF target gene
ChIP-Seq
14 hours ago by shangguandong1996 ▴ 10
0
votes
0
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55
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Comparison of ChIP-seq tracks from two cell lines using FC over control (ENCODE data)
ChIP-seq H3K27ac bigWig ENCODE
13 days ago by erica.fary • 0
7
votes
5
replies
295
views
NovaSeq Duplicates
duplicationrate ChIP-seq
updated 14 days ago by 10k • written 15 days ago by ▴ 10
0
votes
1
reply
116
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Determine the significance of peak overlaps (bedtools)
bedtools peak ChIP-seq eCLIP
updated 16 days ago by 87k • written 17 days ago by ▴ 20
0
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0
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78
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ChIP-seq peak calling with MACS2 - some large peaks for transcription factor
chip-seq macs2 peakcalling
17 days ago by becky.reese17 • 0
1
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3
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1.9k
views
ChromHMM: chromatin states to genome % coverage?
ChIP-Seq ChromHMM
updated 17 days ago by • 0 • written 4.1 years ago by ▴ 10
5
votes
6
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435
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noisy chip-seq peaks
deeptools macs2 chip-seq peaks igv
updated 21 days ago by 9.2k • written 22 days ago by • 0
3
votes
9
replies
534
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Unable to install DiffBind and DESeq2 4.0.3 and 4.0.4 (Package not available on these version of R error)
ChIP-Seq
updated 21 days ago by • 0 • written 4 weeks ago by • 0
0
votes
6
replies
2.9k
views
6 follow
findGenomeMotif.pl in Homer couldn't work properly
ChIP-Seq Homer
updated 23 days ago by • 0 • written 3.6 years ago by • 0
0
votes
0
replies
133
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Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
27 days ago by rintsen.sherpa • 0
0
votes
2
replies
122
views
differential binding analysis of cut-tag peak data
ChIP-Seq
updated 27 days ago by 5.1k • written 27 days ago by • 0
0
votes
1
reply
106
views
why i don not have peak when use DiffBind
ChIP-Seq
27 days ago by 17318598206 • 0
0
votes
1
reply
1.9k
views
No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
ChIP-Seq annotation
updated 28 days ago by • 0 • written 5.5 years ago by ▴ 10
1
vote
2
replies
480
views
Confused about TSS coordinates
ChIP-Seq
updated 29 days ago by • 0 • written 21 months ago by ▴ 40
3
votes
3
replies
121
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How can the assumption of a broad/narrow peak be checked?
macs2 ChIP-Seq
29 days ago by Sam ▴ 160
7
votes
11
replies
2.2k
views
What is the appropriate approach for ChIPseq protein genome occupancy % calculation?
ChIP-Seq
updated 29 days ago by 20 • written 5.8 years ago by ▴ 110
31
votes
34
replies
11k
views
10 follow
How To Randomly Sample A Subset Of Lines From A Bed File
bed chip-seq
updated 29 days ago by ▴ 30 • written 7.5 years ago by ▴ 490
9
votes
6
replies
620
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
ChIP-Seq DiffBind ATAC-seq chipseq diffbind Tool
updated 4 weeks ago by • 0 • written 5 months ago by ★ 1.0k
2
votes
2
replies
102
views
chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions
ChIP-Seq
4 weeks ago by ahadli.farid ▴ 30
0
votes
2
replies
122
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How much sequencing coverage do you need in order to detect SNP's across the whole genome
sequencing SNP ChIP-Seq next-gen
4 weeks ago by dk0319 ▴ 20
2
votes
2
replies
114
views
Diffbind-weird Fold value
ChIP-Seq
updated 4 weeks ago by ★ 1.0k • written 4 weeks ago by • 0
0
votes
0
replies
96
views
A database of cancer super-enhancers
ChIP-Seq super-enhancers cancer
4 weeks ago by MoHallal • 0
1
vote
3
replies
841
views
Can we compare peaks of different transcription factors when they were obtained by different criteria (IDR/FDR)?
ChIP-Seq IDR RNA-Seq
updated 4 weeks ago by 20 • written 2.7 years ago by ▴ 360
3
votes
7
replies
134
views
DiffBind analysis - minCount parameter in dba.count()
ChIP-Seq DiffBind
updated 5 weeks ago by ★ 1.0k • written 5 weeks ago by • 0
0
votes
2
replies
121
views
Bowtie: "Floating point exception: 8"
bowtie alignment ChIP-Seq
updated 5 weeks ago by 9.7k • written 5 weeks ago by ▴ 20
1
vote
1
reply
83
views
How to validate artificially generated enhancers ?
sequencing ChIP-Seq genome machine Learning
5 weeks ago by ahteshamabbasi1996 ▴ 10
1
vote
0
replies
81
views
Integrative analysis of RNA-Seq and Chip-Seq data in R
RNA-Seq ChIP-Seq R
5 weeks ago by g.koorsen ▴ 10
0
votes
9
replies
204
views
The maximum number of peaks in a ChIP-seq data (bigWig format)
ChIP-Seq
5 weeks ago by prgrmmr70 • 0
0
votes
0
replies
90
views
SNPCHIP data analysis
ChIP-Seq genome sequencing
5 weeks ago by arfazevedo • 0
0
votes
1
reply
97
views
DiffBind with duplicates
DiffBind ChIP-Seq
5 weeks ago by jc2842 • 0
0
votes
2
replies
136
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plotCorrelation scatter plot ChIP-seq data
ChIP-Seq deepTools correlation
5 weeks ago by Marco ▴ 20
2
votes
3
replies
126
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Chip-seq balcklisted region information for the latest version of genome ensembl GRCm38
ChIP-Seq alignment
5 weeks ago by luckysardar171 ▴ 10
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
6
votes
4
replies
3.9k
views
Forum: Chip-Seq Data Analysis
chip-seq Forum
updated 5 weeks ago by • 0 • written 8.9 years ago by ★ 1.1k
2
votes
3
replies
186
views
Deeptools plotHeatmap values
ChIP-Seq Deeptools plotHeatmap tables
updated 15 days ago by ▴ 270 • written 5 weeks ago by • 0
3
votes
2
replies
122
views
Cut&Tag / ChIPseq analysis
ChIP-Seq Cut&tag
6 weeks ago by wenbinm ▴ 30
0
votes
0
replies
227
views
Job: Job Posting - Computational Biologist at UTSW
RNA-Seq ChIP-Seq next-gen Job
6 weeks ago by Laura.banaszynski • 0
1
vote
2
replies
122
views
CLIP enrichment analysis
ChIP-Seq
updated 6 weeks ago by 11k • written 6 weeks ago by ▴ 10
5
votes
10
replies
211
views
bamCoverage bin size for narrow and broad histone marks
ChIP-Seq deeptools
6 weeks ago by Marco ▴ 20
0
votes
0
replies
126
views
Correlation heatmap for ChIP-seq data: Pearson or Spearman?
ChIP-Seq correlation deeptools
6 weeks ago by Marco ▴ 20
0
votes
3
replies
150
views
Chip-seq IgG as control or Input DNA or usage of both
ChIP-Seq next-gen sequencing
6 weeks ago by luckysardar171 ▴ 10
0
votes
0
replies
118
views
MultiBigwigSummary of deepTools keeps on running for a long time
ChIP-Seq multibigwigsummary deeptools ubuntu
6 weeks ago by saha.shagnik • 0
2
votes
1
reply
144
views
Interpreting ATAC-SEQ motif enrichment output
ATAC-Seq ChIP-Seq
updated 6 weeks ago by 48k • written 6 weeks ago by • 0
2
votes
4
replies
125
views
Finding Fragment Size chip-seq paired end reads
ChIP-Seq sequencing
6 weeks ago by luckysardar171 ▴ 10
0
votes
2
replies
138
views
Chip_seq analysis remove duplicates
ChIP-Seq
7 weeks ago by luckysardar171 ▴ 10
0
votes
2
replies
258
views
bigWig tracks inconsistent with MACS2 callpeak
ChIP-Seq MACS2
7 weeks ago by lida ▴ 10
2
votes
6
replies
142
views
convert DNA FASTA file to RNA FASTA file
RNA-Seq ChIP-Seq sequence
updated 7 weeks ago by 12k • written 7 weeks ago by ▴ 70
14
votes
10
replies
3.8k
views
from txt to bed
ChIP-Seq
updated 7 weeks ago by 20 • written 4.1 years ago by ▴ 140
0
votes
5
replies
165
views
Pair ended samples cannot map to the genome
ChIP-Seq
7 weeks ago by SayHey • 0
3
votes
3
replies
206
views
Major issue with DiffBind 3?
atac-seq diffbind diffbind3 ChIP-Seq bioconductor
updated 7 weeks ago by ★ 1.0k • written 10 weeks ago by ▴ 20
50 results • Page 1 of 1
Recent Votes
Comment: R - A bioinformatic analysis programming language for NGS
Answer: Finding all instances of a recurring motif in a repeat protein
Answer: Hunting invisible characters?
Comment: Genotype Data in PLINK
Comment: Hunting invisible characters?
Comment: Hunting invisible characters?
Comment: A simple tutorial for a complex ComplexHeatmap
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Comment: Finding all instances of a recurring motif in a repeat protein by NeuralCode • 0
Thanks so much! HMMer is great. Now pulling out hundreds of instances of this domain for my big alignment.
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Using all genes with signed P-value to rank genes, where the sign is from LogFC. and `GSEAPreranked` module in GSEA. ref: [Gene Ranki…
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if you can transform the bed to gff (galaxy has tools for that), you could also use liftoff which wraps all of this in a pipeline https://g…
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Great! Thank you ATpoint
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Another way to see hidden characters is to pipe them through octal dump: `cat infile | od -c` this will print out hidden characters, newlin…
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Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
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It is going to take as long as it takes. You need to be patient and wait until the prompt returns. Based on speed of your CPU/disk things c…
Comment: Hunting invisible characters? by GenoMax 99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
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I'm not sure about three things: What does -M and -O do exactly that could benefit in my case? Why should I specify -t if I don't necessa…
Comment: Hunting invisible characters? by geneticatt ▴ 120
Thank you, using `dos2unix` worked perfectly!
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You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing: dos2unix i5R.txt If an error pops …
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Please do not delete posts that have comments/answers.
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Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
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Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well. [1]: https://j…
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Because this is a plain copy-paste from the novogene page, it has numbers (pointers to specific references that the source has), but not th…
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