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17
votes
34
replies
18k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq demultiplexing
updated 11 months ago by ★ 2.3k • written 7.5 years ago by ▴ 350
0
votes
3
replies
3.7k
views
How to convert Jaspar motif to input into homer?
homer jaspar
updated 2.0 years ago by • 0 • written 6.3 years ago by ▴ 350
3
votes
2
replies
2.6k
views
UMAP of 10X and SmartSeq2 datasets on same plot
smartseq2 singlecellrna-seq umap 10xgenomics
updated 3.9 years ago by 86k • written 3.9 years ago by ▴ 350
18
votes
31
replies
10k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff parse
updated 23 months ago by 9.1k • written 6.4 years ago by ▴ 350
1
vote
3
replies
3.7k
views
Finding differences in motif enrichment between ATAC peak samples?
atac-seq homer
updated 5.4 years ago by ▴ 30 • written 6.3 years ago by ▴ 350
0
votes
1
reply
1.7k
views
Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)
ChIP-Seq
updated 5.5 years ago by ▴ 70 • written 6.2 years ago by ▴ 350
5
votes
4
replies
5.2k
views
How can I find motifs under individual ATAC-peaks?
ATAC-seq
updated 5.5 years ago by ▴ 50 • written 6.4 years ago by ▴ 350
2
votes
1
reply
2.7k
views
TPM normalization factors in RNA-seq
rna-seq
5.8 years ago by a.rex ▴ 350
1
vote
0
replies
1.3k
views
Estimate Library Complexity Output Histogram - what do duplicate sets mean exactly?
picard alignment
5.9 years ago by a.rex ▴ 350
5
votes
3
replies
964
views
How to interpret a short TLEN with 75bp PE seq?
sequence alignment
updated 5.9 years ago by 165k • written 5.9 years ago by ▴ 350
4
votes
8
replies
4.8k
views
Insert size of ~20bp with ATAC-seq?
alignment sequencing atac-seq
updated 5.9 years ago by 86k • written 5.9 years ago by ▴ 350
3
votes
3
replies
1.1k
views
Understanding 9th field of Bam file - insert size?
sequencing alignment
updated 5.9 years ago by 86k • written 5.9 years ago by ▴ 350
5
votes
3
replies
3.0k
views
How can I use featurecounts after generating a bam file using BWA?
RNA-Seq features counts
updated 6.0 years ago by 35k • written 6.0 years ago by ▴ 350
1
vote
0
replies
1.6k
views
How can I get Kimura distances for individual loci from my align.fa file from RepeatMasker
repeatmasker
updated 6.1 years ago by 20 • written 6.2 years ago by ▴ 350
3
votes
3
replies
2.2k
views
Finding motifs with Homer for obscure species.
genome atac-seq homer
updated 6.1 years ago by 20 • written 6.3 years ago by ▴ 350
5
votes
10
replies
4.7k
views
Explaining fragment distribution plots from ATAC-seq
atac-seq
updated 6.1 years ago by 20 • written 6.3 years ago by ▴ 350
4
votes
1
reply
3.1k
views
Using FeatureCounts for ChIP-seq normalised files?
deeptools ChIP-Seq
updated 6.2 years ago by 105k • written 6.2 years ago by ▴ 350
5
votes
6
replies
3.0k
views
Trouble with danpos2 installation - can anyone help?
danpos installation python
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 350
0
votes
0
replies
1.2k
views
Can I use deeptools to calculate nucleosome positions?
deeptools atac
6.2 years ago by a.rex ▴ 350
2
votes
6
replies
3.2k
views
How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K4me1)?
ATAC ChIP
6.2 years ago by a.rex ▴ 350
1
vote
4
replies
3.4k
views
Explaining PCA plots made from BigWig coverage files in DeepTools
deeptools atac-seq
updated 6.2 years ago by 44k • written 6.2 years ago by ▴ 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
6.3 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 6.3 years ago by 36k • written 6.3 years ago by ▴ 350
2
votes
2
replies
1.4k
views
Find unique non overlapping intervals between two files?
bed
updated 6.3 years ago by ★ 5.0k • written 6.3 years ago by ▴ 350
4
votes
3
replies
2.6k
views
Using BedTools to look at unique bed intervals between two files
bedtools
updated 6.3 years ago by 36k • written 6.3 years ago by ▴ 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
6.3 years ago by a.rex ▴ 350
0
votes
1
reply
1.9k
views
Fseq versus MACS2 for ATAC-seq
atac-seq
6.3 years ago by a.rex ▴ 350
17
votes
14
replies
10k
views
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
ATAC-seq next-gen R
updated 6 months ago by ▴ 70 • written 6.3 years ago by ▴ 350
3
votes
4
replies
2.3k
views
Mapping to repeat consensus sequences?
RepeatModeler RepeatMasker
6.4 years ago by a.rex ▴ 350
1
vote
3
replies
1.3k
views
Obtaining list of specific TFs from Interpro tsv file.
Interpro sequence
6.4 years ago by a.rex ▴ 350
2
votes
3
replies
1.6k
views
Comparing genome assemblies of the same animal
Assembly
6.4 years ago by a.rex ▴ 350
4
votes
3
replies
1.1k
views
Perform GO analysis on genome
GO analysis
updated 6.4 years ago by 11k • written 6.4 years ago by ▴ 350
3
votes
1
reply
1.3k
views
How do i extract rows from a bedfile that have a certain bedscore?
bed parse
updated 6.4 years ago by 36k • written 6.4 years ago by ▴ 350
1
vote
2
replies
3.9k
views
How do I perform a motif search on a specific fasta sequence?
homer enhancer
updated 6.4 years ago by 44k • written 6.4 years ago by ▴ 350
5
votes
2
replies
2.1k
views
How to search for TF binding sites upstream of specific genes?
sequence
updated 6.5 years ago by 36k • written 6.5 years ago by ▴ 350
11
votes
8
replies
10.0k
views
6 follow
How do I extract Fasta Sequences based on a list of IDs?
grep sequence
updated 2.7 years ago by 22k • written 6.6 years ago by ▴ 350
6
votes
4
replies
2.0k
views
How find correlations between ChIP-seq tracks?
ChIP-Seq analysis
updated 6.6 years ago by ▴ 480 • written 6.6 years ago by ▴ 350
8
votes
7
replies
6.3k
views
How to compare bigwig tracks of two ATAC libraries.
atac-seq
updated 6.6 years ago by 86k • written 6.6 years ago by ▴ 350
7
votes
5
replies
4.9k
views
How can I look at find 'open chromatin' from ATAC-seq data using MACS2
ATAC-seq MACS2
updated 6.6 years ago by 86k • written 6.6 years ago by ▴ 350
3
votes
7
replies
2.0k
views
How can I map reads only of a certain length?
bwa atac-seq sequencing
updated 6.6 years ago by 165k • written 6.6 years ago by ▴ 350
5
votes
2
replies
4.1k
views
How to demultiplex Unindexed.fastq.gz files?
bcl2fastq illumina
updated 6.6 years ago by 149k • written 6.6 years ago by ▴ 350
0
votes
1
reply
2.1k
views
using gmap to find tss and tes in genome file.
gmap genome transcriptome alignment
updated 6.7 years ago by 20 • written 8.1 years ago by ▴ 350
6
votes
8
replies
4.4k
views
Single - cell RNA-seq analysis - how to look at distribution of gene expression in a t-sne plot?
RNA-Seq
7.1 years ago by a.rex ▴ 350
7
votes
1
reply
2.9k
views
recon issue for repeatmodeler
recon
updated 7.2 years ago by ▴ 90 • written 8.4 years ago by ▴ 350
3
votes
8
replies
14k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
7.3 years ago by a.rex ▴ 350
3
votes
4
replies
3.4k
views
How do I access statistics for read counts after demultiplexing in bcl2fastq?
bcl2fastq
updated 7.5 years ago by 149k • written 7.5 years ago by ▴ 350
0
votes
2
replies
1.4k
views
Separating adapter sequences
ChIP-Seq sequencing
7.7 years ago by a.rex ▴ 350
9
votes
7
replies
3.5k
views
Fetching NCBI ID for a list of species?
gene phylogeny
updated 7.7 years ago by 8.7k • written 7.7 years ago by ▴ 350
3
votes
2
replies
1.7k
views
Extract out fasta sequences using sequence headers.
gene
updated 7.8 years ago by ▴ 840 • written 7.8 years ago by ▴ 350
0
votes
0
replies
1.1k
views
How can I effectively blast lncRNAs against my genome of interest?
blast
7.8 years ago by a.rex ▴ 350
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