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4
votes
6
replies
14k
views
Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
ChIP-Seq
updated 12 weeks ago by ▴ 10 • written 4.2 years ago by ▴ 410
0
votes
1
reply
1.6k
views
findOverlapsOfPeaks() of package ChIPpeakAnno in R
R
updated 4 months ago by • 0 • written 4.3 years ago by ▴ 410
1
vote
3
replies
921
views
Can we compare peaks of different transcription factors when they were obtained by different criteria (IDR/FDR)?
ChIP-Seq IDR RNA-Seq
updated 4 months ago by 20 • written 3.0 years ago by ▴ 410
5
votes
8
replies
618
views
Affymetrix: probeset or transcript cluster?
Affymetrix microarray oligo R
11 months ago by salamandra ▴ 410
2
votes
1
reply
415
views
Summarize by gene for agilent microarray data - one color
R microarray limma
updated 11 months ago by 76k • written 11 months ago by ▴ 410
0
votes
0
replies
322
views
Which annotation package to use to mapIds() on HuEx-1_0-st-v2 microarray platform?
microarray R bioconductor
18 months ago by salamandra ▴ 410
0
votes
2
replies
867
views
Error when reading microarray idat files from illumina
microarray illumina illuminaio R limma
updated 21 months ago by 33k • written 21 months ago by ▴ 410
0
votes
5
replies
1.2k
views
Biopython installation/set path fails in conda env
Biopython
23 months ago by salamandra ▴ 410
1
vote
1
reply
932
views
How to generate a scatter plot of duplication level vs log2reads per kilobase for RNA-seq? (seqmonk)
seqmonk Duplication level RNA-Seq
updated 2.1 years ago by • 0 • written 3.1 years ago by ▴ 410
9
votes
4
replies
1.9k
views
mRNA-seq quality report (fastQC): Does it mean samples have adapters and should remove duplicates?
RNA-Seq fastqc duplicates adapters
updated 2.2 years ago by 20 • written 3.1 years ago by ▴ 410
0
votes
2
replies
2.0k
views
Error in match.arg in boxplot - oligo package
R oligo
updated 2.2 years ago by ★ 1.6k • written 4.3 years ago by ▴ 410
9
votes
4
replies
3.0k
views
BiomaRt: archive version of ensembl not working
biomart r
updated 2.6 years ago by ★ 1.7k • written 2.6 years ago by ▴ 410
7
votes
2
replies
8.6k
views
CPM read count normalization: what does it mean between replicates of same group and within same replicate?
RNA-Seq Read count normalization
updated 2.6 years ago by 52k • written 2.6 years ago by ▴ 410
0
votes
0
replies
1.9k
views
Homer: annotate peaks with ensembl annotation (.gtf) file instead of UCSC anotation file?
homer annotatePeaks.pl
2.6 years ago by salamandra ▴ 410
5
votes
8
replies
3.0k
views
DESeq2 design formula: how to use the opposite interaction term?
deseq2 RNA-Seq
updated 2.6 years ago by 76k • written 2.7 years ago by ▴ 410
15
votes
12
replies
4.7k
views
BioMart: connection fails
BioMart
2.7 years ago by salamandra ▴ 410
7
votes
9
replies
3.3k
views
How does MACS algorithm work on ATAC-seq data if there is no control sample and no model estimation?
ChIP-Seq MACS
updated 2.7 years ago by • 0 • written 3.7 years ago by ▴ 410
5
votes
2
replies
1.2k
views
Difference between affy_hg_u133a and with_affy_hg_u133a
R Biomart
updated 2.8 years ago by 20 • written 4.3 years ago by ▴ 410
3
votes
8
replies
3.3k
views
ValueError: invalid literal for int() with base 10: 'start' computeMatrix of deeptools
ChIP-Seq Deeptools
updated 2.9 years ago by 34k • written 4.1 years ago by ▴ 410
0
votes
0
replies
1.2k
views
degPatterns: Error in lower.to.upper.tri.inds(n) : 'n' must be >= 2
RNA-seq clustering
2.9 years ago by salamandra ▴ 410
4
votes
8
replies
1.2k
views
Tool that can split genes into groups with similar expression pattern overtime and plot them?
RNA-Seq clustering
updated 2.9 years ago by ▴ 50 • written 2.9 years ago by ▴ 410
1
vote
1
reply
446
views
How to automatically retrieve genes of preselected enzymes in a pathway map?
gene
updated 3.0 years ago by ▴ 300 • written 3.0 years ago by ▴ 410
8
votes
8
replies
1.6k
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 3.0 years ago by 76k • written 3.0 years ago by ▴ 410
4
votes
14
replies
1.4k
views
Deseq2: What is the most correct experimental design for this experiment?
Deseq2 experimental design RNA-seq
updated 3.0 years ago by 99k • written 3.0 years ago by ▴ 410
3
votes
2
replies
2.8k
views
Homer error (findMotifs.pl) : are you sure you chose the right length for motif finding?
Chip-seq motifs homer
updated 3.0 years ago by 76k • written 3.0 years ago by ▴ 410
4
votes
4
replies
1.1k
views
How to mask motif in HOMER?
mask motif chip-seq homer
updated 3.0 years ago by 76k • written 3.0 years ago by ▴ 410
3
votes
14
replies
2.3k
views
How to use a specific promoter set on findMotifs.pl of HOMER?
ChIP-Seq HOMER promoter set motifs
updated 3.0 years ago by 76k • written 3.0 years ago by ▴ 410
0
votes
0
replies
1.0k
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
3.0 years ago by salamandra ▴ 410
4
votes
3
replies
662
views
Why when splitting file in two we add 1 line before dividing the number of lines by 2?
split commandline bash
3.0 years ago by salamandra ▴ 410
2
votes
4
replies
2.0k
views
RNA-seq: Should remove duplicates in all samples of same experiment although some do not have technical duplicates?
RNA-Seq duplication dupRadar
updated 3.0 years ago by 33k • written 3.1 years ago by ▴ 410
2
votes
1
reply
1.2k
views
How to calculate effective genome size using unique-kmers.py from khmer program?
effective genome size khmer ChIP-Seq
3.0 years ago by salamandra ▴ 410
1
vote
1
reply
1.1k
views
What parameter values to change in peak calling with MACS2 when calculating IDR afterwards?
ChIP-Seq MACS2 IDR
3.0 years ago by salamandra ▴ 410
2
votes
4
replies
780
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 3.0 years ago by 99k • written 3.0 years ago by ▴ 410
4
votes
4
replies
2.0k
views
What is chr EBV in human sam file?
SAM Bowtie2
updated 3.0 years ago by 104k • written 3.0 years ago by ▴ 410
0
votes
0
replies
1.0k
views
What tool should be used to determine IDR or Np/Nt and N1/N2 between ChIP-seq samples?
ChIP-Seq IDR ENCODE
3.0 years ago by salamandra ▴ 410
1
vote
1
reply
1.6k
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
3.0 years ago by salamandra ▴ 410
3
votes
1
reply
1.2k
views
RNA-seq: Can we obtain distances between samples of different experiments?
RNA-Seq sample clustering
updated 3.0 years ago by 33k • written 3.0 years ago by ▴ 410
9
votes
4
replies
3.0k
views
Questions regarding VST/rlog correction to plot sample distances between RNA-seq samples
RNA-Seq R DEseq
updated 3.0 years ago by 76k • written 3.0 years ago by ▴ 410
5
votes
2
replies
887
views
Does importing HTseqcounts with txtimport corrects for gene length?
RNA-Seq deseq R
updated 3.0 years ago by 99k • written 3.0 years ago by ▴ 410
3
votes
13
replies
4.1k
views
Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with commandline/with R dupRadar package
markduplicates Picard RNA-Seq
3.1 years ago by salamandra ▴ 410
2
votes
1
reply
467
views
Seqmonk has two CRCh38 human genome versions, which one is the major release?
assembly RNA-seq genome ensembl
3.1 years ago by salamandra ▴ 410
4
votes
6
replies
3.8k
views
STAR ERROR: could not open genomeParameters.txt / How to increase RAM?
STAR RNA-Seq
3.1 years ago by salamandra ▴ 410
2
votes
2
replies
4.1k
views
STAR alignment error: Genome_genomeGenerate.cpp:208:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir/
RNA-Seq STAR
3.1 years ago by salamandra ▴ 410
2
votes
4
replies
865
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
3.1 years ago by salamandra ▴ 410
14
votes
14
replies
8.5k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
3.1 years ago by salamandra ▴ 410
10
votes
11
replies
2.9k
views
Does adapter removal (with trimmomatic) also remove barcodes?
barcodes adapters RNA-Seq
updated 3.1 years ago by 10k • written 3.1 years ago by ▴ 410
1
vote
3
replies
1.5k
views
Error: could not find function "exptData"
R
updated 3.2 years ago by • 0 • written 4.3 years ago by ▴ 410
2
votes
6
replies
1.8k
views
Isn't fastq file header suppose to have barcode sequence?
ChIP-Seq Quality control
updated 3.3 years ago by 20 • written 3.5 years ago by ▴ 410
16
votes
11
replies
4.7k
views
6 follow
If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
ChIP-Seq Duplicates MACS2
updated 3.4 years ago by 20 • written 3.4 years ago by ▴ 410
0
votes
0
replies
819
views
Beedtools intersect: more peaks intersected than intersected portions of those peaks?
beedtools intersect sequencing RNA-seq ChIP-seq
3.4 years ago by salamandra ▴ 410
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