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Showing :
questions
2
votes
3
replies
2.2k
views
Gold standard for bulk RNA-seq downsampling - number of uniquely mapped reads
uniquely
RNA-seq
mapping
bulk
downsampling
3.0 years ago by
msimmer92
▴ 300
9
votes
4
replies
5.6k
views
How to filter out a list of specific genes from the DESeq object in R - bulk RNA-seq differential expression
R
bulk
object
DESeq2
filter
3.0 years ago by
msimmer92
▴ 300
0
votes
3
replies
1.7k
views
Generalizing snakemake MACS2 code - WildcardError Wildcards in input files cannot be determined from output files: 'sample'
snakemake
updated 4.0 years ago by
Jeremy Leipzig
22k • written 4.1 years ago by
msimmer92
▴ 300
5
votes
4
replies
3.8k
views
Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/cwl in rule
snakemake
syntaxerror
rule
keywords
4.1 years ago by
msimmer92
▴ 300
2
votes
3
replies
1.7k
views
Heterogeneity from bulk ChIP-seq or ATAC-seq data
heterogeneity
ChIP-seq
ATAC-seq
clustering
updated 4.5 years ago by
jared.andrews07
★ 16k • written 4.5 years ago by
msimmer92
▴ 300
7
votes
7
replies
2.8k
views
Downsampling single-end human ChIP-seq data
ChIP-Seq
downsampling
subsampling
updated 4.9 years ago by
colin.kern
★ 1.1k • written 4.9 years ago by
msimmer92
▴ 300
4
votes
7
replies
2.5k
views
How to properly organize a DiffBind analysis to normalize data across conditions (ChIP-seq)
diffbind
R
ChIP-Seq
updated 4.9 years ago by
ATpoint
82k • written 4.9 years ago by
msimmer92
▴ 300
6
votes
5
replies
2.2k
views
How to zoom out to whole genome view in UCSC browser?
UCSC
browser
bigWig
5.0 years ago by
msimmer92
▴ 300
1
vote
1
reply
2.1k
views
How to interpret fast or multiQC reports of easy HiC or HiC data
HiC
easyHiC
fastqc
5.0 years ago by
msimmer92
▴ 300
2
votes
2
replies
2.8k
views
Can bedtools subtract support multiple files?
bedtools
5.1 years ago by
msimmer92
▴ 300
3
votes
8
replies
9.2k
views
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
R
DiffBind
ChIP-Seq
5.1 years ago by
msimmer92
▴ 300
0
votes
1
reply
1.7k
views
R's DiffBind. Error in pv.DBAplotVolcano(DBA, contrast = contrast, method = method,: object 'sigSites' not found
DiffBind
R
ChIP-Seq
updated 5.2 years ago by
Friederike
8.9k • written 5.2 years ago by
msimmer92
▴ 300
4
votes
10
replies
3.6k
views
Unexpected hump in GC content distribution from FasQC report in ChIP-seq
ChIP-Seq
fastqc
quality
5.2 years ago by
msimmer92
▴ 300
10
votes
12
replies
2.0k
views
The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
genes
human
housekeeping
list
5.2 years ago by
msimmer92
▴ 300
6
votes
6
replies
8.6k
views
How to subset reads from fastq file to use as test file on a script
bash
fastq
subset
sample
written 5.3 years ago by
msimmer92
▴ 300
23
votes
7
replies
5.8k
views
Is blacklisted regions filtering in ChIP-seq still needed? (let's talk about the state of the art)
blacklist
ChIP-Seq
filtering
updated 5.3 years ago by
Devon Ryan
104k • written 5.3 years ago by
msimmer92
▴ 300
10
votes
14
replies
9.8k
views
Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
BAM
SAM
MAPQ
quality
filtering
5.3 years ago by
msimmer92
▴ 300
0
votes
1
reply
2.0k
views
Nothing happens when I type jellyfish histo mer_counts.jf - command fails to produce k-mer histogram
RNA-Seq
6.1 years ago by
msimmer92
▴ 300
3
votes
2
replies
3.4k
views
Trimmomatic 0.36 not acknowledging commands in MacOS terminal in SE mode
software-error
RNA-Seq
updated 10 months ago by
Ram
43k • written 6.1 years ago by
msimmer92
▴ 300
7
votes
6
replies
3.6k
views
Error: --fst requires at least two nonempty clusters.
Plink
updated 11 months ago by
dre.gaudio
• 0 • written 6.9 years ago by
msimmer92
▴ 300
8
votes
2
replies
15k
views
Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens than expected
plink
updated 7.0 years ago by
willgilks
▴ 360 • written 7.0 years ago by
msimmer92
▴ 300
0
votes
0
replies
1.7k
views
Can't find the "classic" error in merged vcf files with vcf-merge.
vcf
vcf-merge
7.1 years ago by
msimmer92
▴ 300
22 results • Page
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