Limit : all time
all time today this week this month this year
90,325 results • Page 1 of 1807
Sort: Rank
Rank Views Votes Replies
Filtering for tag: ChIP-Seq • reset
0
votes
0
replies
45
views
Comparison of ChIP-seq tracks from two cell lines using FC over control (ENCODE data)
ChIP-seq H3K27ac bigWig ENCODE
9 days ago by erica.fary • 0
7
votes
5
replies
262
views
NovaSeq Duplicates
duplicationrate ChIP-seq
updated 10 days ago by 10k • written 11 days ago by ▴ 10
0
votes
1
reply
105
views
Determine the significance of peak overlaps (bedtools)
bedtools peak ChIP-seq eCLIP
updated 12 days ago by 87k • written 12 days ago by ▴ 20
0
votes
0
replies
68
views
ChIP-seq peak calling with MACS2 - some large peaks for transcription factor
chip-seq macs2 peakcalling
12 days ago by becky.reese17 • 0
1
vote
3
replies
1.9k
views
ChromHMM: chromatin states to genome % coverage?
ChIP-Seq ChromHMM
updated 12 days ago by • 0 • written 4.1 years ago by ▴ 10
5
votes
6
replies
402
views
noisy chip-seq peaks
deeptools macs2 chip-seq peaks igv
updated 16 days ago by 9.2k • written 17 days ago by • 0
3
votes
9
replies
495
views
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 17 days ago by • 0 • written 25 days ago by • 0
0
votes
6
replies
2.8k
views
6 follow
findGenomeMotif.pl in Homer couldn't work properly
ChIP-Seq Homer
updated 18 days ago by • 0 • written 3.6 years ago by • 0
0
votes
0
replies
121
views
Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
22 days ago by rintsen.sherpa • 0
0
votes
2
replies
115
views
differential binding analysis of cut-tag peak data
ChIP-Seq
updated 23 days ago by 5.1k • written 23 days ago by • 0
0
votes
1
reply
96
views
why i don not have peak when use DiffBind
ChIP-Seq
23 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 23 days ago by • 0 • written 5.5 years ago by ▴ 10
1
vote
2
replies
476
views
Confused about TSS coordinates
ChIP-Seq
updated 24 days ago by • 0 • written 21 months ago by ▴ 40
3
votes
3
replies
112
views
How can the assumption of a broad/narrow peak be checked?
macs2 ChIP-Seq
25 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 25 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 25 days ago by ▴ 30 • written 7.4 years ago by ▴ 490
9
votes
6
replies
593
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
ChIP-Seq DiffBind ATAC-seq chipseq diffbind Tool
updated 25 days ago by • 0 • written 5 months ago by ★ 1.0k
2
votes
2
replies
95
views
chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions
ChIP-Seq
25 days ago by ahadli.farid ▴ 30
0
votes
2
replies
115
views
How much sequencing coverage do you need in order to detect SNP's across the whole genome
sequencing SNP ChIP-Seq next-gen
25 days ago by dk0319 ▴ 20
2
votes
2
replies
106
views
Diffbind-weird Fold value
ChIP-Seq
updated 26 days ago by ★ 1.0k • written 26 days ago by • 0
0
votes
0
replies
88
views
A database of cancer super-enhancers
ChIP-Seq super-enhancers cancer
26 days ago by MoHallal • 0
1
vote
3
replies
834
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
126
views
DiffBind analysis - minCount parameter in dba.count()
ChIP-Seq DiffBind
updated 4 weeks ago by ★ 1.0k • written 4 weeks ago by • 0
0
votes
2
replies
114
views
Bowtie: "Floating point exception: 8"
bowtie alignment ChIP-Seq
updated 4 weeks ago by 9.7k • written 4 weeks ago by ▴ 20
1
vote
1
reply
79
views
How to validate artificially generated enhancers ?
sequencing ChIP-Seq genome machine Learning
4 weeks ago by ahteshamabbasi1996 ▴ 10
1
vote
0
replies
77
views
Integrative analysis of RNA-Seq and Chip-Seq data in R
RNA-Seq ChIP-Seq R
4 weeks ago by g.koorsen ▴ 10
0
votes
9
replies
199
views
The maximum number of peaks in a ChIP-seq data (bigWig format)
ChIP-Seq
4 weeks ago by prgrmmr70 • 0
0
votes
0
replies
87
views
SNPCHIP data analysis
ChIP-Seq genome sequencing
4 weeks ago by arfazevedo • 0
0
votes
1
reply
90
views
DiffBind with duplicates
DiffBind ChIP-Seq
4 weeks ago by jc2842 • 0
0
votes
2
replies
129
views
plotCorrelation scatter plot ChIP-seq data
ChIP-Seq deepTools correlation
4 weeks ago by Marco ▴ 20
2
votes
3
replies
122
views
Chip-seq balcklisted region information for the latest version of genome ensembl GRCm38
ChIP-Seq alignment
4 weeks ago by luckysardar171 ▴ 10
0
votes
0
replies
101
views
converting bedgraph to Bigwig by HOMER
HOMER bedGraph BigWig bioinformatics ChIP-seq
4 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
172
views
Deeptools plotHeatmap values
ChIP-Seq Deeptools plotHeatmap tables
updated 11 days ago by ▴ 270 • written 5 weeks ago by • 0
3
votes
2
replies
114
views
Cut&Tag / ChIPseq analysis
ChIP-Seq Cut&tag
5 weeks ago by wenbinm ▴ 30
0
votes
0
replies
217
views
Job: Job Posting - Computational Biologist at UTSW
RNA-Seq ChIP-Seq next-gen Job
5 weeks ago by Laura.banaszynski • 0
1
vote
2
replies
118
views
CLIP enrichment analysis
ChIP-Seq
updated 5 weeks ago by 11k • written 5 weeks ago by ▴ 10
5
votes
10
replies
199
views
bamCoverage bin size for narrow and broad histone marks
ChIP-Seq deeptools
5 weeks ago by Marco ▴ 20
0
votes
0
replies
118
views
Correlation heatmap for ChIP-seq data: Pearson or Spearman?
ChIP-Seq correlation deeptools
5 weeks ago by Marco ▴ 20
0
votes
3
replies
143
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
109
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
131
views
Interpreting ATAC-SEQ motif enrichment output
ATAC-Seq ChIP-Seq
updated 6 weeks ago by 47k • written 6 weeks ago by • 0
2
votes
4
replies
118
views
Finding Fragment Size chip-seq paired end reads
ChIP-Seq sequencing
6 weeks ago by luckysardar171 ▴ 10
0
votes
2
replies
134
views
Chip_seq analysis remove duplicates
ChIP-Seq
6 weeks ago by luckysardar171 ▴ 10
0
votes
2
replies
248
views
bigWig tracks inconsistent with MACS2 callpeak
ChIP-Seq MACS2
6 weeks ago by lida ▴ 10
2
votes
6
replies
126
views
convert DNA FASTA file to RNA FASTA file
RNA-Seq ChIP-Seq sequence
updated 6 weeks ago by 12k • written 6 weeks ago by ▴ 70
14
votes
10
replies
3.8k
views
from txt to bed
ChIP-Seq
updated 6 weeks ago by 20 • written 4.1 years ago by ▴ 140
0
votes
5
replies
160
views
Pair ended samples cannot map to the genome
ChIP-Seq
7 weeks ago by SayHey • 0
3
votes
3
replies
197
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
18
votes
12
replies
3.7k
views
Removal of repeat and blacklist regions from ChIP-seq data
ChIP-Seq Blacklist ENCODE
updated 7 weeks ago by 20 • written 4.1 years ago by ★ 3.1k
90,325 results • Page 1 of 1807
Recent Votes
Answer: RNAseq data analysis of pooled data
Comment: RNAseq data analysis of pooled data
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
A: How to select lines (filter) in vcf files that have same genotypes for all the s
A: How to select lines (filter) in vcf files that have same genotypes for all the s
A: What Do You Waste Your Time On
Comment: RNAseq data analysis of pooled data
Recent Locations • All
Bengaluru, just now
Tehran, just now
Argentina, just now
Texas, just now
France/Nantes/Institut du Thorax - INSERM UMR1087, 1 minute ago
Israel, 3 minutes ago
University Park, USA, 3 minutes ago
Recent Awards • All
Teacher to andrew.j.skelton73 6.2k
Scholar to Devon Ryan 98k
Supporter to David_emir ▴ 390
Good Answer to Philipp Bayer 6.9k
Voter to Thomas ▴ 100
Scholar to rpazo001 ▴ 10
Supporter to i.sudbery 11k
Recent Replies
Comment: Finding how many times a nucleotide appear in the same position by cpad0112 15k
#!/usr/bin/env python3 sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGG…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database by Anand Rao ▴ 350
Thanks for your reply. Yes, I think I could have explained my problem much better, but rather than change my original post, I will add some…
Answer: Finding how many times a nucleotide appear in the same position by Dunois ▴ 600
Here's a little `python` function you can work off of: def count_quer_at_pos_in_seq(seqs, quer = "A"): #Initialize a list…
Comment: Using outgroup in gene family dendograms by Rogerio Ribeiro ▴ 50
Thank for the fast reponse. The ABC family is not the best example for this question indeed. The objective of my work is to find genes resp…
Answer: Taxonomy assignment of viral RNA by Zhilong Jia ★ 1.7k
1. Blast directly 2. [IDSeq][1], can get viral contigs and their annotation directly. [IDSeq : An open-source cloud-based pipeline and…
Comment: Finding how many times a nucleotide appear in the same position by hugo.avila ▴ 180
Hi, It is not a norm but it is a good practice to post an attempted resolution first and then other members try to correct it or suggest an…
Comment: What Do You Waste Your Time On by ponganta ▴ 150
Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.
Answer: What Do You Waste Your Time On by ponganta ▴ 150
Reinventing the wheel. Like, all the time. Why use clusterProfiler with an up-to-date GO-annotation, when you can just write your own clien…
Comment: RNAseq data analysis of pooled data by ponganta ▴ 150
By "pooled" data, do you mean data from tissue-specific bulk-RNAseq? Or did you pool single cell (SC) RNAseq-libraries?
Comment: RNAseq data analysis of pooled data by Dunois ▴ 600
What exactly do you mean by "pooled" data?
Answer: RNAseq data analysis of pooled data by grant.hovhannisyan ★ 2.1k
I made a tutorial last year for University students on this topic https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7. Let me know …
Comment: RNAseq data analysis of pooled data by luffy • 0
@dunois Thank you for the tutorial, what are your thoughts for approach for pooled data? should i follow the documentation/the tutorial or …
Comment: How to extract only the specific fasta sequences by matching the ID's to a diff by pinn ▴ 90
In my case, it doesn't work. parallel --verbose 'echo "TRINITY_{}" > test__.txt | seqtk subseq /home/sunn/data/softwares/evaluation/Tr…
Comment: How to extract all columns of CSQ using split-vep plugin of bcftools? by Pierre Lindenbaum 135k
> extract all of them as table using is this plugin able to convert vcf to a tabular format ?
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens by GenoMax 99k
> How do I get one-to-one transcript ID mapping? I don't think you will get that pre-computed. You will need to perhaps align the transcr…
Traffic: 1398 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