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7
votes
5
replies
3.6k
views
What is chr EBV in human sam file?
SAM Bowtie2
written 6.4 years ago by ▴ 550
4
votes
9
replies
6.7k
views
ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
ChIP-Seq Deeptools
updated 2.3 years ago by • 0 • written 7.5 years ago by ▴ 550
2
votes
3
replies
6.4k
views
STAR alignment error: Genome_genomeGenerate.cpp:208:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir/
RNA-Seq STAR
updated 2.6 years ago by • 0 • written 6.5 years ago by ▴ 550
0
votes
1
reply
2.5k
views
findOverlapsOfPeaks in ChIPpeakAnno R package
R ChIP-Seq
updated 2.7 years ago by ▴ 10 • written 7.7 years ago by ▴ 550
5
votes
6
replies
27k
views
Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
ChIP-Seq
updated 3.6 years ago by ▴ 20 • written 7.5 years ago by ▴ 550
0
votes
1
reply
2.7k
views
findOverlapsOfPeaks() of package ChIPpeakAnno in R
R
updated 3.7 years ago by ▴ 10 • written 7.7 years ago by ▴ 550
1
vote
3
replies
2.0k
views
Can we compare peaks of different transcription factors when they were obtained by different criteria (IDR/FDR)?
ChIP-Seq IDR RNA-Seq
updated 3.7 years ago by 20 • written 6.4 years ago by ▴ 550
5
votes
8
replies
2.8k
views
Affymetrix: probeset or transcript cluster?
Affymetrix microarray oligo R
4.3 years ago by salamandra ▴ 550
2
votes
1
reply
1.3k
views
Summarize by gene for agilent microarray data - one color
R microarray limma
updated 4.3 years ago by 88k • written 4.3 years ago by ▴ 550
0
votes
2
replies
2.1k
views
Error when reading microarray idat files from illumina
microarray illumina illuminaio R limma
updated 5.2 years ago by 35k • written 5.2 years ago by ▴ 550
1
vote
5
replies
3.6k
views
Biopython installation/set path fails in conda env
Biopython
5.3 years ago by salamandra ▴ 550
1
vote
1
reply
1.8k
views
How to generate a scatter plot of duplication level vs log2reads per kilobase for RNA-seq? (seqmonk)
seqmonk Duplication level RNA-Seq
updated 5.4 years ago by • 0 • written 6.4 years ago by ▴ 550
9
votes
4
replies
3.4k
views
mRNA-seq quality report (fastQC): Does it mean samples have adapters and should remove duplicates?
RNA-Seq fastqc duplicates adapters
updated 5.6 years ago by 20 • written 6.5 years ago by ▴ 550
0
votes
2
replies
3.3k
views
Error in match.arg in boxplot - oligo package
R oligo
updated 5.6 years ago by ★ 1.6k • written 7.7 years ago by ▴ 550
14
votes
4
replies
6.8k
views
BiomaRt: archive version of ensembl not working
biomart r
updated 5.9 years ago by ★ 2.1k • written 5.9 years ago by ▴ 550
9
votes
2
replies
17k
views
CPM read count normalization: what does it mean between replicates of same group and within same replicate?
RNA-Seq Read count normalization
updated 5.9 years ago by 85k • written 5.9 years ago by ▴ 550
20
votes
8
replies
8.8k
views
DESeq2 design formula: how to use the opposite interaction term?
deseq2 RNA-Seq
updated 6.0 years ago by 88k • written 6.0 years ago by ▴ 550
16
votes
12
replies
15k
views
BioMart: connection fails
BioMart
6.1 years ago by salamandra ▴ 550
8
votes
9
replies
6.1k
views
How does MACS algorithm work on ATAC-seq data if there is no control sample and no model estimation?
ChIP-Seq MACS
updated 6.1 years ago by • 0 • written 7.1 years ago by ▴ 550
5
votes
2
replies
2.2k
views
Difference between affy_hg_u133a and with_affy_hg_u133a
R Biomart
updated 6.2 years ago by 20 • written 7.7 years ago by ▴ 550
4
votes
8
replies
2.9k
views
Tool that can split genes into groups with similar expression pattern overtime and plot them?
RNA-Seq clustering
updated 6.3 years ago by ▴ 60 • written 6.3 years ago by ▴ 550
1
vote
1
reply
813
views
How to automatically retrieve genes of preselected enzymes in a pathway map?
gene
updated 6.3 years ago by ▴ 300 • written 6.3 years ago by ▴ 550
9
votes
8
replies
3.4k
views
7 follow
Know if a pathway is being functionally activated or repressed by a group of up-regulated genes
RNA-Seq text-mining gene set enrichment
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 550
4
votes
14
replies
2.9k
views
Deseq2: What is the most correct experimental design for this experiment?
Deseq2 experimental design RNA-seq
updated 6.3 years ago by 104k • written 6.3 years ago by ▴ 550
3
votes
2
replies
6.5k
views
Homer error (findMotifs.pl) : are you sure you chose the right length for motif finding?
Chip-seq motifs homer
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 550
4
votes
4
replies
2.3k
views
How to mask motif in HOMER?
mask motif chip-seq homer
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 550
3
votes
14
replies
5.3k
views
How to use a specific promoter set on findMotifs.pl of HOMER?
ChIP-Seq HOMER promoter set motifs
updated 6.3 years ago by 88k • written 6.3 years ago by ▴ 550
0
votes
0
replies
1.8k
views
ChIP-seq: To use IDR, samples have to pass both tests or is it enough to pass the pseudo-replicate test?
ChIP-Seq IDR
6.3 years ago by salamandra ▴ 550
4
votes
3
replies
1.4k
views
Why when splitting file in two we add 1 line before dividing the number of lines by 2?
split commandline bash
6.3 years ago by salamandra ▴ 550
2
votes
4
replies
3.9k
views
RNA-seq: Should remove duplicates in all samples of same experiment although some do not have technical duplicates?
RNA-Seq duplication dupRadar
updated 6.3 years ago by 35k • written 6.4 years ago by ▴ 550
3
votes
1
reply
2.4k
views
How to calculate effective genome size using unique-kmers.py from khmer program?
effective genome size khmer ChIP-Seq
6.4 years ago by salamandra ▴ 550
1
vote
1
reply
2.0k
views
What parameter values to change in peak calling with MACS2 when calculating IDR afterwards?
ChIP-Seq MACS2 IDR
6.4 years ago by salamandra ▴ 550
2
votes
4
replies
1.5k
views
Does Bowtie2 index use haplotypes and patches? and is the reference genome of Bowtie2 from UCSC or ensembl?
ChIP-Seq haplotypes scaffolds Bowtie2 ensembl
updated 6.4 years ago by 104k • written 6.4 years ago by ▴ 550
0
votes
0
replies
1.8k
views
What tool should be used to determine IDR or Np/Nt and N1/N2 between ChIP-seq samples?
ChIP-Seq IDR ENCODE
6.4 years ago by salamandra ▴ 550
1
vote
1
reply
3.0k
views
How to select a gene annotation file in ensembl that contain un-localized scaffolds, but NO patches or haplotypes?
assembly RNA-Seq STAR genome
6.4 years ago by salamandra ▴ 550
3
votes
1
reply
1.7k
views
RNA-seq: Can we obtain distances between samples of different experiments?
RNA-Seq sample clustering
updated 6.4 years ago by 35k • written 6.4 years ago by ▴ 550
11
votes
4
replies
5.2k
views
Questions regarding VST/rlog correction to plot sample distances between RNA-seq samples
RNA-Seq R DEseq
updated 6.4 years ago by 88k • written 6.4 years ago by ▴ 550
5
votes
2
replies
1.9k
views
Does importing HTseqcounts with txtimport corrects for gene length?
RNA-Seq deseq R
updated 6.4 years ago by 104k • written 6.4 years ago by ▴ 550
3
votes
13
replies
9.5k
views
Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with commandline/with R dupRadar package
markduplicates Picard RNA-Seq
6.4 years ago by salamandra ▴ 550
2
votes
1
reply
900
views
Seqmonk has two CRCh38 human genome versions, which one is the major release?
assembly RNA-seq genome ensembl
6.4 years ago by salamandra ▴ 550
4
votes
6
replies
6.5k
views
STAR ERROR: could not open genomeParameters.txt / How to increase RAM?
STAR RNA-Seq
6.4 years ago by salamandra ▴ 550
2
votes
4
replies
1.5k
views
Which gene annotation file in UCSC is equivalent to the gene annotation file that is NOT 'abinitio' or 'chromossome' in ensembl?
RNA-Seq anotation file
6.5 years ago by salamandra ▴ 550
16
votes
14
replies
18k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
6.5 years ago by salamandra ▴ 550
10
votes
11
replies
5.8k
views
Does adapter removal (with trimmomatic) also remove barcodes?
barcodes adapters RNA-Seq
updated 6.5 years ago by 14k • written 6.5 years ago by ▴ 550
1
vote
3
replies
2.5k
views
Error: could not find function "exptData"
R
updated 6.5 years ago by • 0 • written 7.7 years ago by ▴ 550
3
votes
6
replies
3.5k
views
Isn't fastq file header suppose to have barcode sequence?
ChIP-Seq Quality control
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 550
20
votes
11
replies
9.7k
views
6 follow
If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
ChIP-Seq Duplicates MACS2
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 550
0
votes
0
replies
1.3k
views
Beedtools intersect: more peaks intersected than intersected portions of those peaks?
beedtools intersect sequencing RNA-seq ChIP-seq
6.7 years ago by salamandra ▴ 550
3
votes
7
replies
5.5k
views
Why command gives the error: extra operand 23243?
commandline Bash comm
6.7 years ago by salamandra ▴ 550
1
vote
4
replies
4.6k
views
Deeptools - ComputeMatrix: Why does 'referencePoint center' gives the same heatmap as 'referencePoint TSS'
ChIP-Seq sequencing deeptools
6.8 years ago by salamandra ▴ 550
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