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17
votes
34
replies
19k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq demultiplexing
updated 14 months ago by ★ 2.4k • written 7.8 years ago by ▴ 350
0
votes
3
replies
3.9k
views
How to convert Jaspar motif to input into homer?
homer jaspar
updated 2.3 years ago by • 0 • written 6.5 years ago by ▴ 350
3
votes
2
replies
2.7k
views
UMAP of 10X and SmartSeq2 datasets on same plot
smartseq2 singlecellrna-seq umap 10xgenomics
updated 4.2 years ago by 88k • written 4.2 years ago by ▴ 350
18
votes
31
replies
11k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff parse
updated 2.1 years ago by 9.2k • written 6.6 years ago by ▴ 350
1
vote
3
replies
3.8k
views
Finding differences in motif enrichment between ATAC peak samples?
atac-seq homer
updated 5.7 years ago by ▴ 30 • written 6.6 years ago by ▴ 350
0
votes
1
reply
1.8k
views
Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)
ChIP-Seq
updated 5.8 years ago by ▴ 70 • written 6.5 years ago by ▴ 350
5
votes
4
replies
5.3k
views
How can I find motifs under individual ATAC-peaks?
ATAC-seq
updated 5.8 years ago by ▴ 50 • written 6.6 years ago by ▴ 350
2
votes
1
reply
2.8k
views
TPM normalization factors in RNA-seq
rna-seq
6.0 years ago by a.rex ▴ 350
1
vote
0
replies
1.3k
views
Estimate Library Complexity Output Histogram - what do duplicate sets mean exactly?
picard alignment
6.2 years ago by a.rex ▴ 350
5
votes
3
replies
1.0k
views
How to interpret a short TLEN with 75bp PE seq?
sequence alignment
updated 6.2 years ago by 166k • written 6.2 years ago by ▴ 350
4
votes
8
replies
5.1k
views
Insert size of ~20bp with ATAC-seq?
alignment sequencing atac-seq
updated 6.2 years ago by 88k • written 6.2 years ago by ▴ 350
0
votes
1
reply
5.1k
views
Comment: C: Insert size of -20bp with ATAC-seq?
6.2 years ago by a.rex ▴ 350
0
votes
1
reply
5.1k
views
Comment: C: Insert size of -20bp with ATAC-seq?
6.2 years ago by a.rex ▴ 350
3
votes
3
replies
1.2k
views
Understanding 9th field of Bam file - insert size?
sequencing alignment
updated 6.2 years ago by 88k • written 6.2 years ago by ▴ 350
0
votes
0
replies
5.1k
views
Comment: A: Insert size of -20bp with ATAC-seq?
6.2 years ago by a.rex ▴ 350
0
votes
0
replies
5.1k
views
Comment: C: Insert size of -20bp with ATAC-seq?
6.2 years ago by a.rex ▴ 350
5
votes
3
replies
3.1k
views
How can I use featurecounts after generating a bam file using BWA?
RNA-Seq features counts
updated 6.3 years ago by 35k • written 6.3 years ago by ▴ 350
1
vote
0
replies
1.6k
views
How can I get Kimura distances for individual loci from my align.fa file from RepeatMasker
repeatmasker
updated 6.4 years ago by 20 • written 6.5 years ago by ▴ 350
3
votes
3
replies
2.2k
views
Finding motifs with Homer for obscure species.
genome atac-seq homer
updated 6.4 years ago by 20 • written 6.6 years ago by ▴ 350
5
votes
10
replies
4.9k
views
Explaining fragment distribution plots from ATAC-seq
atac-seq
updated 6.4 years ago by 20 • written 6.6 years ago by ▴ 350
4
votes
1
reply
3.2k
views
Using FeatureCounts for ChIP-seq normalised files?
deeptools ChIP-Seq
updated 6.5 years ago by 105k • written 6.5 years ago by ▴ 350
5
votes
6
replies
3.1k
views
Trouble with danpos2 installation - can anyone help?
danpos installation python
updated 6.5 years ago by 35k • written 6.5 years ago by ▴ 350
0
votes
1
reply
3.1k
views
Comment: C: Trouble with danpos2 installation - can anyone help?
6.5 years ago by a.rex ▴ 350
0
votes
1
reply
3.1k
views
Comment: C: Trouble with danpos2 installation - can anyone help?
6.5 years ago by a.rex ▴ 350
0
votes
0
replies
1.3k
views
Can I use deeptools to calculate nucleosome positions?
deeptools atac
6.5 years ago by a.rex ▴ 350
0
votes
0
replies
3.4k
views
Comment: C: How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K
6.5 years ago by a.rex ▴ 350
2
votes
6
replies
3.4k
views
How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K4me1)?
ATAC ChIP
6.5 years ago by a.rex ▴ 350
1
vote
4
replies
3.6k
views
Explaining PCA plots made from BigWig coverage files in DeepTools
deeptools atac-seq
updated 6.5 years ago by 45k • written 6.5 years ago by ▴ 350
0
votes
2
replies
3.6k
views
Comment: C: Explaining PCA plots made from BigWig coverage files in DeepTools
6.5 years ago by a.rex ▴ 350
0
votes
1
reply
1.3k
views
Is it common for ATAC-peaks to be located in Repeat Masker annotated regions?
genome atac-seq
6.5 years ago by a.rex ▴ 350
3
votes
1
reply
1.4k
views
Finding common peaks between F-seq peak region files
fseq atac
updated 6.5 years ago by 36k • written 6.5 years ago by ▴ 350
2
votes
2
replies
1.5k
views
Find unique non overlapping intervals between two files?
bed
updated 6.5 years ago by ★ 5.0k • written 6.5 years ago by ▴ 350
4
votes
3
replies
2.7k
views
Using BedTools to look at unique bed intervals between two files
bedtools
updated 6.6 years ago by 36k • written 6.6 years ago by ▴ 350
0
votes
0
replies
1.1k
views
What should I choose to best specify background sequences when looking for motifs under peaks in Homer?
Homer
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
2.2k
views
Comment: C: Finding motifs with Homer for obscure species.
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
2.0k
views
Fseq versus MACS2 for ATAC-seq
atac-seq
6.6 years ago by a.rex ▴ 350
0
votes
0
replies
5.1k
views
Comment: C: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
6.6 years ago by a.rex ▴ 350
0
votes
0
replies
4.9k
views
Comment: C: Explaining fragment distribution plots from ATAC-seq
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
4.9k
views
Comment: C: Explaining fragment distribution plots from ATAC-seq
6.6 years ago by a.rex ▴ 350
0
votes
0
replies
4.9k
views
Comment: C: Explaining fragment distribution plots from ATAC-seq
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
11k
views
Comment: C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.6 years ago by a.rex ▴ 350
0
votes
2
replies
11k
views
Comment: C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
11k
views
Comment: C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
11k
views
Comment: C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
11k
views
Comment: C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
11k
views
Comment: C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.6 years ago by a.rex ▴ 350
17
votes
14
replies
11k
views
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
ATAC-seq next-gen R
updated 9 months ago by ▴ 70 • written 6.6 years ago by ▴ 350
0
votes
0
replies
3.8k
views
Comment: C: Finding differences in motif enrichment between ATAC peak samples?
6.6 years ago by a.rex ▴ 350
0
votes
0
replies
2.5k
views
Comment: C: Mapping to repeat consensus sequences?
6.6 years ago by a.rex ▴ 350
0
votes
1
reply
2.5k
views
Comment: C: Mapping to repeat consensus sequences?
6.6 years ago by a.rex ▴ 350
130 results • Page 1 of 3
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