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90,325 results • Page
1 of 1807
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Filtering for tag:
ChIP-Seq
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0
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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
lieven.sterck
10k • written 11 days ago by
trio.qbm
▴ 10
0
votes
1
reply
105
views
Determine the significance of peak overlaps (bedtools)
bedtools
peak
ChIP-seq
eCLIP
updated 12 days ago by
Istvan Albert
87k • written 12 days ago by
kstangline
▴ 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
Yussuf
• 0 • written 4.1 years ago by
Sy80
▴ 10
5
votes
6
replies
402
views
noisy chip-seq peaks
deeptools
macs2
chip-seq
peaks
igv
updated 16 days ago by
jared.andrews07
9.2k • written 17 days ago by
kolikolmakani14
• 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
MK
• 0 • written 25 days ago by
tiptophamza
• 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
Fleur
• 0 • written 3.6 years ago by
xuenjun1
• 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
rpolicastro
5.1k • written 23 days ago by
17318598206
• 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
hukai916
• 0 • written 5.5 years ago by
MarcinKosinski
▴ 10
1
vote
2
replies
476
views
Confused about TSS coordinates
ChIP-Seq
updated 24 days ago by
Zhenpeng Yu
• 0 • written 21 months ago by
srhic
▴ 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
Biostar
20 • written 5.8 years ago by
AlexAbdulkaderKheirallah
▴ 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
cjgunase
▴ 30 • written 7.4 years ago by
bede.portz
▴ 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
shuwanli
• 0 • written 5 months ago by
Rory Stark
★ 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
Rory Stark
★ 1.0k • written 26 days ago by
wei.zhang
• 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
Biostar
20 • written 2.7 years ago by
salamandra
▴ 360
3
votes
7
replies
126
views
DiffBind analysis - minCount parameter in dba.count()
ChIP-Seq
DiffBind
updated 4 weeks ago by
Rory Stark
★ 1.0k • written 4 weeks ago by
vartika
• 0
0
votes
2
replies
114
views
Bowtie: "Floating point exception: 8"
bowtie
alignment
ChIP-Seq
updated 4 weeks ago by
swbarnes2
9.7k • written 4 weeks ago by
Marco
▴ 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
prgrmmr70
• 0 • written 8.9 years ago by
Raony Guimarães
★ 1.1k
2
votes
3
replies
172
views
Deeptools plotHeatmap values
ChIP-Seq
Deeptools
plotHeatmap
tables
updated 11 days ago by
2nelly
▴ 270 • written 5 weeks ago by
saha.shagnik
• 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
i.sudbery
11k • written 5 weeks ago by
noahhelton98
▴ 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
ATpoint
47k • written 6 weeks ago by
emalekos
• 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
JC
12k • written 6 weeks ago by
xiaoleiusc
▴ 70
14
votes
10
replies
3.8k
views
from txt to bed
ChIP-Seq
updated 6 weeks ago by
Biostar
20 • written 4.1 years ago by
dimitrischat
▴ 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
Rory Stark
★ 1.0k • written 10 weeks ago by
musaddeque.ahmed
▴ 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
Biostar
20 • written 4.1 years ago by
James Ashmore
★ 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
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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
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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…
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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…
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