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17
votes
34
replies
18k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 9 months ago by
barslmn
★ 2.3k • written 7.4 years ago by
a.rex
▴ 350
0
votes
3
replies
3.6k
views
How to convert Jaspar motif to input into homer?
homer
jaspar
updated 22 months ago by
carinapaola20
• 0 • written 6.1 years ago by
a.rex
▴ 350
3
votes
2
replies
2.6k
views
UMAP of 10X and SmartSeq2 datasets on same plot
smartseq2
singlecellrna-seq
umap
10xgenomics
updated 3.7 years ago by
ATpoint
86k • written 3.7 years ago by
a.rex
▴ 350
18
votes
31
replies
9.7k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff
parse
updated 20 months ago by
Juke34
8.9k • written 6.2 years ago by
a.rex
▴ 350
1
vote
3
replies
3.6k
views
Finding differences in motif enrichment between ATAC peak samples?
atac-seq
homer
updated 5.2 years ago by
danvoronov
▴ 30 • written 6.2 years ago by
a.rex
▴ 350
0
votes
1
reply
1.7k
views
Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)
ChIP-Seq
updated 5.3 years ago by
Jingyue
▴ 70 • written 6.1 years ago by
a.rex
▴ 350
5
votes
4
replies
5.0k
views
How can I find motifs under individual ATAC-peaks?
ATAC-seq
updated 5.4 years ago by
gable_works
▴ 50 • written 6.2 years ago by
a.rex
▴ 350
2
votes
1
reply
2.6k
views
TPM normalization factors in RNA-seq
rna-seq
5.6 years ago by
a.rex
▴ 350
1
vote
0
replies
1.2k
views
Estimate Library Complexity Output Histogram - what do duplicate sets mean exactly?
picard
alignment
5.7 years ago by
a.rex
▴ 350
5
votes
3
replies
914
views
How to interpret a short TLEN with 75bp PE seq?
sequence
alignment
updated 5.7 years ago by
Pierre Lindenbaum
164k • written 5.7 years ago by
a.rex
▴ 350
4
votes
8
replies
4.6k
views
Insert size of ~20bp with ATAC-seq?
alignment
sequencing
atac-seq
updated 5.7 years ago by
ATpoint
86k • written 5.7 years ago by
a.rex
▴ 350
0
votes
1
reply
4.6k
views
Comment:
C: Insert size of -20bp with ATAC-seq?
5.7 years ago by
a.rex
▴ 350
0
votes
1
reply
4.6k
views
Comment:
C: Insert size of -20bp with ATAC-seq?
5.7 years ago by
a.rex
▴ 350
3
votes
3
replies
1.1k
views
Understanding 9th field of Bam file - insert size?
sequencing
alignment
updated 5.7 years ago by
ATpoint
86k • written 5.7 years ago by
a.rex
▴ 350
0
votes
0
replies
4.6k
views
Comment:
A: Insert size of -20bp with ATAC-seq?
5.7 years ago by
a.rex
▴ 350
0
votes
0
replies
4.6k
views
Comment:
C: Insert size of -20bp with ATAC-seq?
5.7 years ago by
a.rex
▴ 350
5
votes
3
replies
2.9k
views
How can I use featurecounts after generating a bam file using BWA?
RNA-Seq
features counts
updated 5.8 years ago by
h.mon
35k • written 5.8 years ago by
a.rex
▴ 350
1
vote
0
replies
1.5k
views
How can I get Kimura distances for individual loci from my align.fa file from RepeatMasker
repeatmasker
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
a.rex
▴ 350
3
votes
3
replies
2.0k
views
Finding motifs with Homer for obscure species.
genome
atac-seq
homer
updated 6.0 years ago by
Biostar
20 • written 6.1 years ago by
a.rex
▴ 350
5
votes
10
replies
4.5k
views
Explaining fragment distribution plots from ATAC-seq
atac-seq
updated 6.0 years ago by
Biostar
20 • written 6.1 years ago by
a.rex
▴ 350
4
votes
1
reply
3.0k
views
Using FeatureCounts for ChIP-seq normalised files?
deeptools
ChIP-Seq
updated 6.1 years ago by
Devon Ryan
104k • written 6.1 years ago by
a.rex
▴ 350
5
votes
6
replies
2.8k
views
Trouble with danpos2 installation - can anyone help?
danpos
installation
python
updated 6.1 years ago by
h.mon
35k • written 6.1 years ago by
a.rex
▴ 350
0
votes
1
reply
2.8k
views
Comment:
C: Trouble with danpos2 installation - can anyone help?
6.1 years ago by
a.rex
▴ 350
0
votes
1
reply
2.8k
views
Comment:
C: Trouble with danpos2 installation - can anyone help?
6.1 years ago by
a.rex
▴ 350
0
votes
0
replies
1.2k
views
Can I use deeptools to calculate nucleosome positions?
deeptools
atac
6.1 years ago by
a.rex
▴ 350
0
votes
0
replies
3.1k
views
Comment:
C: How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K
6.1 years ago by
a.rex
▴ 350
2
votes
6
replies
3.1k
views
How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K4me1)?
ATAC
ChIP
6.1 years ago by
a.rex
▴ 350
1
vote
4
replies
3.3k
views
Explaining PCA plots made from BigWig coverage files in DeepTools
deeptools
atac-seq
updated 6.1 years ago by
Ram
44k • written 6.1 years ago by
a.rex
▴ 350
0
votes
2
replies
3.3k
views
Comment:
C: Explaining PCA plots made from BigWig coverage files in DeepTools
6.1 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
6.1 years ago by
a.rex
▴ 350
3
votes
1
reply
1.3k
views
Finding common peaks between F-seq peak region files
fseq
atac
updated 6.1 years ago by
Alex Reynolds
36k • written 6.1 years ago by
a.rex
▴ 350
2
votes
2
replies
1.4k
views
Find unique non overlapping intervals between two files?
bed
updated 6.1 years ago by
harold.smith.tarheel
★ 5.0k • written 6.1 years ago by
a.rex
▴ 350
4
votes
3
replies
2.6k
views
Using BedTools to look at unique bed intervals between two files
bedtools
updated 6.1 years ago by
Alex Reynolds
36k • written 6.1 years ago by
a.rex
▴ 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
6.1 years ago by
a.rex
▴ 350
0
votes
1
reply
2.0k
views
Comment:
C: Finding motifs with Homer for obscure species.
6.1 years ago by
a.rex
▴ 350
0
votes
1
reply
1.9k
views
Fseq versus MACS2 for ATAC-seq
atac-seq
6.1 years ago by
a.rex
▴ 350
0
votes
0
replies
4.8k
views
Comment:
C: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
6.1 years ago by
a.rex
▴ 350
0
votes
0
replies
4.5k
views
Comment:
C: Explaining fragment distribution plots from ATAC-seq
6.1 years ago by
a.rex
▴ 350
0
votes
1
reply
4.5k
views
Comment:
C: Explaining fragment distribution plots from ATAC-seq
6.1 years ago by
a.rex
▴ 350
0
votes
0
replies
4.5k
views
Comment:
C: Explaining fragment distribution plots from ATAC-seq
6.1 years ago by
a.rex
▴ 350
0
votes
1
reply
9.6k
views
Comment:
C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.2 years ago by
a.rex
▴ 350
0
votes
2
replies
9.6k
views
Comment:
C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.2 years ago by
a.rex
▴ 350
0
votes
1
reply
9.6k
views
Comment:
C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.2 years ago by
a.rex
▴ 350
0
votes
1
reply
9.6k
views
Comment:
C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.2 years ago by
a.rex
▴ 350
0
votes
1
reply
9.6k
views
Comment:
C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.2 years ago by
a.rex
▴ 350
0
votes
1
reply
9.6k
views
Comment:
C: Using featureCounts and DESeq2 to look at differences between ATAC-seq condition
6.2 years ago by
a.rex
▴ 350
17
votes
14
replies
9.6k
views
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
ATAC-seq
next-gen
R
updated 4 months ago by
QX
▴ 60 • written 6.2 years ago by
a.rex
▴ 350
0
votes
0
replies
3.6k
views
Comment:
C: Finding differences in motif enrichment between ATAC peak samples?
6.2 years ago by
a.rex
▴ 350
0
votes
0
replies
2.2k
views
Comment:
C: Mapping to repeat consensus sequences?
6.2 years ago by
a.rex
▴ 350
0
votes
1
reply
2.2k
views
Comment:
C: Mapping to repeat consensus sequences?
6.2 years ago by
a.rex
▴ 350
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