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questions
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.2 years ago by
biostart
▴ 370
0
votes
9
replies
2.0k
views
Bowtie paired-end mapping: insert size issue
alignment
mapping
bowtie
updated 2.3 years ago by
GenoMax
142k • written 2.3 years ago by
biostart
▴ 370
3
votes
2
replies
831
views
Mapping SRA files without unpacking?
alignment
Bowtie
SRA
sequencing
updated 2.6 years ago by
ATpoint
82k • written 2.6 years ago by
biostart
▴ 370
3
votes
9
replies
3.6k
views
7 follow
Gene Ontology without enrichment analysis
next-gen
RNA-Seq
ChIP-Seq
updated 4.4 years ago by
yairgatt
▴ 10 • written 8.2 years ago by
biostart
▴ 370
4
votes
9
replies
1.8k
views
Correlation of two ChIP-seq signals?
ChIP-Seq
updated 4.4 years ago by
Prakash
★ 2.2k • written 4.5 years ago by
biostart
▴ 370
0
votes
11
replies
2.1k
views
Problem mapping paired-end Illumina reads
ChIP-Seq
alignment
paired-end
updated 5.4 years ago by
swbarnes2
14k • written 5.4 years ago by
biostart
▴ 370
3
votes
1
reply
2.5k
views
How to create BigWig files with normalised signal using ChIP-seq and Input?
ChIP-Seq
BigWig
updated 5.4 years ago by
Devon Ryan
104k • written 5.4 years ago by
biostart
▴ 370
2
votes
0
replies
1.1k
views
Heatmaps of bisulfite sequencing data
heatmap
methylation
5.5 years ago by
biostart
▴ 370
1
vote
1
reply
1.7k
views
HOMER works incorrectly with -sspe option for paired-end reads
ChIP-Seq
HOMER
updated 5.8 years ago by
Kevin Blighe
88k • written 5.8 years ago by
biostart
▴ 370
1
vote
3
replies
2.2k
views
MACS peak calling of paired-end reads in SAM format
ChIP-Seq
MACS
SAM
5.8 years ago by
biostart
▴ 370
5
votes
9
replies
4.2k
views
6 follow
Peak calling for broad histone-modification regions
ChIP-Seq
updated 7.0 years ago by
Rashedul Islam
▴ 470 • written 7.0 years ago by
biostart
▴ 370
2
votes
3
replies
5.0k
views
What's the name in RepeatMasker for mouse major satellite repeats?
sequence
alignment
RNA-Seq
updated 7.1 years ago by
Mike
▴ 60 • written 7.2 years ago by
biostart
▴ 370
0
votes
5
replies
2.9k
views
Motif finding with HOMER
ChIP-Seq
sequencing
motif
pwm
7.5 years ago by
biostart
▴ 370
1
vote
2
replies
2.8k
views
Are HOMER aggregate proflles normalized to the read depth of each ChIP-seq sample? [still open]
ChIP-Seq
sequencing
updated 7.5 years ago by
Biostar
20 • written 8.3 years ago by
biostart
▴ 370
6
votes
10
replies
3.6k
views
Statistical test to compare the number of upregulated genes in a subgroup of genes versus all genes?
rna-seq
updated 7.6 years ago by
vakul.mohanty
▴ 270 • written 7.6 years ago by
biostart
▴ 370
2
votes
7
replies
3.2k
views
Statistical test to compare expression change in a subgroup of genes versus all genes?
RNA-Seq
updated 7.6 years ago by
h.mon
35k • written 7.6 years ago by
biostart
▴ 370
2
votes
8
replies
2.9k
views
Mann-Whitney test -- is it applicable to compare log2 fold change in a subset of genes to all genes?
RNA-Seq
7.6 years ago by
biostart
▴ 370
9
votes
10
replies
2.3k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
7.7 years ago by
biostart
▴ 370
4
votes
4
replies
2.3k
views
Converting CpG methylation calls to average genome coverage
DNA methylation
BS-seq
updated 8.0 years ago by
Biostar
20 • written 8.1 years ago by
biostart
▴ 370
1
vote
4
replies
3.0k
views
[solved] Bowtie mapping paired-end reads of different length
ChIP-Seq
8.1 years ago by
biostart
▴ 370
0
votes
1
reply
2.9k
views
bedtools closest (output file format)
bedtools
RNA-Seq
ChIP-Seq
updated 8.2 years ago by
Alex Reynolds
35k • written 8.2 years ago by
biostart
▴ 370
3
votes
7
replies
2.4k
views
Separating gene list into chromatin domains and analysing separately within each domain
RNA-Seq
ChIP-Seq
Hi-C
updated 8.2 years ago by
Alex Reynolds
35k • written 8.2 years ago by
biostart
▴ 370
1
vote
2
replies
2.1k
views
Problem mapping SOLiD reads with Bowtie1
sequencing
ChIP-Seq
updated 22 months ago by
Ram
44k • written 8.3 years ago by
biostart
▴ 370
5
votes
5
replies
7.4k
views
How to calculate enrichment P-value?
ChIP-Seq
updated 22 months ago by
Ram
44k • written 8.3 years ago by
biostart
▴ 370
6
votes
3
replies
5.5k
views
BedTools can't find "hg19.genome"
ChIP-Seq
updated 8.3 years ago by
GenoMax
142k • written 8.3 years ago by
biostart
▴ 370
5
votes
19
replies
5.5k
views
Merging many BAM files [solved]
next-gen
ChIP-Seq
rna-seq
updated 22 months ago by
Ram
44k • written 8.3 years ago by
biostart
▴ 370
2
votes
1
reply
3.1k
views
Can I use HOMER to create a tag dir from a 400 Gb BAM file?
RNA-Seq
ChIP-Seq
updated 8.3 years ago by
Sukhi Singh
11k • written 8.3 years ago by
biostart
▴ 370
3
votes
9
replies
2.3k
views
SOLiD reads unreadable to Bowtie after unpacking from .sra archive [still open]
ChIP-Seq
alignment
updated 2.1 years ago by
Ram
44k • written 8.4 years ago by
biostart
▴ 370
4
votes
4
replies
4.7k
views
Splice site coordinates: where to get them?
RNA-Seq
ChIP-Seq
sequence
next-gen
updated 8.3 years ago by
Sean Davis
27k • written 8.4 years ago by
biostart
▴ 370
0
votes
4
replies
2.4k
views
Is it typical to find a ~30 bp motif enriched in promoters of ~20 related genes?
ChIP-Seq
motif
promoter
enhancer
rna-seq
updated 2.2 years ago by
Ram
44k • written 9.4 years ago by
biostart
▴ 370
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