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Showing top results for tag: ChIP-Seq • reset
0
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3
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437
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Job:  Graduate student position in bioinformatics available at the University of Iowa
genome next-gen ChIP-Seq RNA-Seq SNP Job
updated 9 hours ago by • 0 • written 6 months ago by • 0
0
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2
replies
83
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  BED Heatmap
ChIP-seq
updated 1 day ago by 33k • written 1 day ago by ▴ 30
0
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0
replies
41
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  HOMER annotatepeaks.pl
ChIP-Seq HOMER sequencing next-gen
2 days ago by jjp55 ▴ 20
1
vote
2
replies
102
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  Different peak sites from .xls and .narrowPeak, macs2 output
diffbind atac-seq macs2 chip-seq callpeak
2 days ago by sh.kazempour94 • 0
0
votes
1
reply
402
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  MACS2 error in fragment size estimation from paired-end STAR-aligned RNA-seq data
ChIP-Seq software alignment RNA-Seq error
updated 12 days ago by 50k • written 11 months ago by • 0
0
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1
reply
73
views
  SICER2 (or EPIC) genomes
Genome EPIC ChIP-seq SICER Sequencing
updated 12 days ago by 50k • written 13 days ago by ▴ 20
0
votes
8
replies
383
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  DiffBind 3.2 error
DiffBind R ChIP-seq
12 days ago by Huang Zhihao • 0
0
votes
4
replies
158
views
  deeptools 3.5 plotCorrelation
ChIP-Seq sequencing plotCorrelation next-gen deeptools
updated 14 days ago by 6.4k • written 14 days ago by ▴ 20
1
vote
2
replies
130
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  call peaks of single-end mapping bam files
ChIP-Seq alignment error software genome
16 days ago by szp770 ▴ 10
0
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0
replies
98
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  Scaling HOMER tag directories
ChIP-seq Next HOMER Generation Sequencing
18 days ago by jjp55 ▴ 20
3
votes
2
replies
199
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News:  New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
DiffBind ChIP-seq deepTools visualization ATAC-seq
1 day ago by Rory Stark ★ 1.1k
1
vote
1
reply
200
views
  Comparing differentially expressed peaks to get unique values
ATAC-seq diffbind ChIP-Seq Genomic Ranges
updated 22 days ago by ★ 1.1k • written 4 months ago by ▴ 10
0
votes
4
replies
171
views
  struct.error in MACS2 callpeak
ChIP-seq MACS2
23 days ago by ty0017 • 0
0
votes
1
reply
99
views
  Power calculation for RIP-seq
RIP-seq CHIP-seq
updated 25 days ago by 50k • written 25 days ago by ▴ 30
0
votes
0
replies
48
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  HOMER average conservation information
homermotif peaks chip-seq annotation motifanalysis
26 days ago by buffealo ▴ 10
0
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0
replies
65
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  Chipseq allelic density plot for TSS region
Chip-Seq Allelic-Chipseq Deeptools
28 days ago by BISEP • 0
0
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2
replies
186
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  No peaks in CUT&RUN
bowtie2 ngs chip-seq SEACR
4 weeks ago by Johanna • 0
0
votes
11
replies
366
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  different sequencing depths for Input and IP in ChIP-Seq
depth ChIP-Seq sequencing normalisation
5 weeks ago by Genestar • 0
6
votes
8
replies
3.7k
views
  Modeling Chip-Seq Background Using Edger'S Glm Functionality?
chip-seq edger
updated 5 weeks ago by 50k • written 8.8 years ago by ★ 3.5k
0
votes
2
replies
148
views
  Understanding PCA plot from DiffBind
diffbind pca chip-seq
updated 5 weeks ago by ★ 1.1k • written 5 weeks ago by ▴ 20
1
vote
1
reply
84
views
  single- indexed sequenced as paired end
Chip-seq NGS Illumina
updated 5 weeks ago by 102k • written 5 weeks ago by ▴ 20
0
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4
replies
239
views
  Preparing ChIP-seq data for analysis with DESeq2
DESeq2 ChIP-seq
5 weeks ago by gkunz ▴ 10
3
votes
6
replies
14k
views
  Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
ChIP-Seq
updated 5 weeks ago by • 0 • written 4.0 years ago by ▴ 390
3
votes
9
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5.9k
views
  question about macs2 --broad-cutoff
ChIP-Seq MACS2 macs2 broadpeak broad-cutoff
5 weeks ago by Yu ▴ 110
0
votes
0
replies
86
views
  DiffBind3 outputs compared to previous versions
DiffBind3 R ChIP-seq EdgeR Deseq2
6 weeks ago by gkunz ▴ 10
0
votes
0
replies
106
views
  Enhancer region
Chip-seq enhancer
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
4
replies
180
views
  trim_galore error: Cutadapt terminated with exit signal: '256'
RNA-seq cutadapt chip-seq sequencing trimgalore
6 weeks ago by szp770 ▴ 10
0
votes
1
reply
329
views
  Gene locations do not match
ChIP-Seq
updated 7 weeks ago by 50k • written 5 months ago by • 0
0
votes
1
reply
328
views
  ChIPSeeker Help for Annotating Peaks
ChIP-Seq atac-seq software error
updated 7 weeks ago by ▴ 70 • written 6 months ago by • 0
4
votes
8
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321
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  How to extend ChIP-seq reads from BAM file ?
read-extension NGS ChIP-seq
7 weeks ago by jseg • 0
3
votes
7
replies
433
views
  Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak calling?
R ChIP-seq ChIPQC
updated 8 weeks ago by 12k • written 8 weeks ago by ▴ 10
0
votes
1
reply
184
views
  How to get GSE data into IGV
ChIP-Seq IGV GSE
updated 8 weeks ago by ▴ 80 • written 8 weeks ago by • 0
0
votes
3
replies
245
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  DiffBind consensus peak extraction
DiffBind ChIP-seq
updated 8 weeks ago by ★ 1.1k • written 8 weeks ago by • 0
0
votes
0
replies
515
views
  how to combined peak score or other quantitative indicator when identify TF target gene
ChIP-Seq
8 weeks ago by shangguandong1996 ▴ 10
0
votes
0
replies
119
views
  Comparison of ChIP-seq tracks from two cell lines using FC over control (ENCODE data)
ChIP-seq H3K27ac bigWig ENCODE
10 weeks ago by erica.fary • 0
7
votes
5
replies
471
views
  NovaSeq Duplicates
duplicationrate ChIP-seq
updated 10 weeks ago by 11k • written 11 weeks ago by ▴ 10
0
votes
1
reply
216
views
  Determine the significance of peak overlaps (bedtools)
bedtools peak ChIP-seq eCLIP
updated 11 weeks ago by 88k • written 11 weeks ago by ▴ 30
0
votes
0
replies
134
views
  ChIP-seq peak calling with MACS2 - some large peaks for transcription factor
chip-seq macs2 peakcalling
11 weeks ago by becky.reese17 • 0
1
vote
3
replies
2.0k
views
  ChromHMM: chromatin states to genome % coverage?
ChIP-Seq ChromHMM
updated 11 weeks ago by • 0 • written 4.3 years ago by ▴ 10
5
votes
6
replies
611
views
  noisy chip-seq peaks
deeptools macs2 chip-seq peaks igv
updated 11 weeks ago by ★ 10k • written 11 weeks ago by • 0
3
votes
9
replies
695
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 11 weeks ago by • 0 • written 3 months ago by • 0
0
votes
6
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3.0k
views
6 follow
  findGenomeMotif.pl in Homer couldn't work properly
ChIP-Seq Homer
updated 12 weeks ago by • 0 • written 3.8 years ago by • 0
0
votes
0
replies
185
views
  Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
12 weeks ago by rintsen.sherpa • 0
0
votes
2
replies
171
views
  differential binding analysis of cut-tag peak data
ChIP-Seq
updated 12 weeks ago by 5.3k • written 12 weeks ago by • 0
0
votes
1
reply
146
views
  why i don not have peak when use DiffBind
ChIP-Seq
12 weeks 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 12 weeks ago by • 0 • written 5.7 years ago by ▴ 10
1
vote
2
replies
541
views
  Confused about TSS coordinates
ChIP-Seq
updated 3 months ago by • 0 • written 23 months ago by ▴ 40
3
votes
3
replies
169
views
  How can the assumption of a broad/narrow peak be checked?
macs2 ChIP-Seq
3 months ago by Sam ▴ 170
7
votes
11
replies
2.2k
views
  What is the appropriate approach for ChIPseq protein genome occupancy % calculation?
ChIP-Seq
updated 3 months ago by 20 • written 6.0 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 3 months ago by ▴ 30 • written 7.6 years ago by ▴ 490
50 results • Page 1 of 1
Recent Votes
ELI5: Different methods to analyse differential expression other than limma?
Comment: flye assembly stuck on 'Aligning reads to the graph'
Answer: Orthologs vs PFAM
Answer: Orthologs vs PFAM
flye assembly stuck on 'Aligning reads to the graph'
flye assembly stuck on 'Aligning reads to the graph'
Orthologs vs PFAM
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Recent Replies
Comment: Computational Biologist position at the University of Alabama at Birmingham by lianov • 0
Thank you @cpad0112 for your comment. Indeed UAB requests all the information from the screenshot which you have attached. However, most of…
Comment: flye assembly stuck on 'Aligning reads to the graph' by GenoMax 102k
That is good to know. You can also make use of those short reads to make sure there are no unexpected indels etc in your long read assembli…
Comment: problem: i try to merge reads with seqprep but is not working by GenoMax 102k
You can try the method suggested here to estimate size of inserts in your library: https://www.biostars.org/p/223897/#223916 It is not nece…
Comment: Orthologs vs PFAM by timothy.kirkwood ▴ 40
Ah very interesting, thanks for your comment! Would you consider all members of a Pfam (= a protein family, not a superfamily, unless I mi…
Comment: Diffbind3 dba.plotMA error by francesca3 ▴ 40
Hi Rory, I'm having the same problems with some of my analyses. After reading here, I downloaded the latest version of DiffBind but the err…
Comment: Velocyto: Not found cell and umi barcode in entry of the bam file by lb58 • 0
This is the begining of the fastq file that I have >head ./H9_D4/SRR9117954_S1_L001_R1_001.fastq @SRR9117954.1 A00291:31:H5W5MDMXX…
Comment: Velocyto: Not found cell and umi barcode in entry of the bam file by Nitin Narwade ▴ 680
Probably the SRA data does not have UMI/Barcode sequence in the header. You can check that information in the fastq header.
Comment: Installing an updated R version (>=4.0) using conda by Nitin Narwade ▴ 680
Do you mean, you are trying to run `R` and getting the error `segmentation fault (core dumped)` OR running some command on the `R` interpre…
Comment: Where I can download o/e scores in gnomad files? by Ram 33k
Have you tried looking at the VCF files? What are "o/e scores" by the way?
Answer: hg38 coordinates for centromeric, subtelomeric and telomeric regions by Pierre Lindenbaum 136k
same as https://www.biostars.org/p/2349/ , replace hg18 with hg38
Comment: Multifactor Design For RNA-seq Analysis by David Martínez • 0
Thank you for your comments.
Comment: Orthologs vs PFAM by Mensur Dlakic ★ 11k
I think when they started Pfam, the idea was to have entries for individual protein families - thus the name. This in turn means that the i…
Comment: Orthologs vs PFAM by Mensur Dlakic ★ 11k
> but that also means you can't say that all orthologs share a common function The way I always thought about this is that all orthologs d…
Answer: LOW BUSCO Score for De novo genome assembly by Mensur Dlakic ★ 11k
For a complex genome such as the one you work with, it is most likely impossible to get a complete assembly with short reads and 50x covera…
Comment: Orthologs vs PFAM by lieven.sterck 11k
mmyez :) indeed, if we consider orthology implies shared function that is an assumption/proximisation we made. In most cases this will ho…
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