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0
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2
replies
1.5k
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Question about HOMER peak annotation to some features. Customize gff3?
ChIP-Seq HOMER annotation
3.3 years ago by nanoide ▴ 120
3
votes
3
replies
886
views
Recommendations on FAIRE-seq/ATAC-seq optimal coverage for large genome
ATAC-seq FAIRE-seq Coverage
3.4 years ago by nanoide ▴ 120
10
votes
9
replies
1.3k
views
Help interpretating DESeq2 output
Deseq2 Fold-Change RNA-seq
updated 7 months ago by 43k • written 3.4 years ago by ▴ 120
0
votes
0
replies
863
views
Trying to compile the software seqoutbias with cargo within a conda environment
rust cargo seqoutbias compilation
3.6 years ago by nanoide ▴ 120
0
votes
0
replies
872
views
Some question on HGAP installation and use
genome assembly HGAP PacBio
3.9 years ago by nanoide ▴ 120
2
votes
3
replies
1.3k
views
How to add a flag to a sam/bam file
ATAC-seq samtools flag filtering
updated 4.1 years ago by 20 • written 4.2 years ago by ▴ 120
9
votes
9
replies
4.7k
views
ATAC-seq TSS profile plot interpretation
ATAC-seq TSS V-plot
4.4 years ago by nanoide ▴ 120
1
vote
1
reply
2.2k
views
HaplotypeCallerSpark How to use
snp GATK
updated 4.6 years ago by 5.8k • written 4.6 years ago by ▴ 120
6
votes
4
replies
3.1k
views
Merging the output of salmon for RNA-seq counting with paired-end and single-end reads simultaneously
RNA-Seq single-end paired-end salmon
4.7 years ago by nanoide ▴ 120
4
votes
0
replies
2.3k
views
Peak annotation with HOMER. Statistics with the annStats parameter
ChIP-seq HOMER annotatePeaks.pl stats
4.8 years ago by nanoide ▴ 120
19
votes
6
replies
8.0k
views
samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
ATAC-seq samtools Markduplicates
updated 4.8 years ago by ★ 1.9k • written 4.8 years ago by ▴ 120
2
votes
2
replies
2.4k
views
Question about ChromHMM overlap enrichment
ChromHMM ChIP-Seq segmentation
updated 4.9 years ago by ▴ 130 • written 5.8 years ago by ▴ 120
0
votes
0
replies
1.2k
views
ATACseqQC factorFootprints function
ATACseqQC ATAC-seq footprint
4.9 years ago by nanoide ▴ 120
0
votes
0
replies
1.6k
views
Help filling the configuration file for the masurca assembler
illumina Assembly masurca fastqc pacbio
5.0 years ago by nanoide ▴ 120
6
votes
3
replies
2.1k
views
Question about exon/intron counting in RNA-seq dataset analysis
RNA-Seq htseq-count featureCounts
updated 5.0 years ago by 14k • written 5.0 years ago by ▴ 120
1
vote
1
reply
1.0k
views
Is it possible to control the coordinate of the peak that HOMER takes into account to annotate?
ChIP-seq macs2 peaks homer annotation
updated 5.0 years ago by ★ 16k • written 5.0 years ago by ▴ 120
12
votes
13
replies
5.9k
views
Running STAR aligner with paired-end and single-end reads simultaneously
STAR RNA-Seq paired-end single-end
5.1 years ago by nanoide ▴ 120
4
votes
1
reply
2.4k
views
Converting motif databases from meme suite to other formats
meme motif format
updated 5.1 years ago by 35k • written 5.1 years ago by ▴ 120
7
votes
4
replies
2.0k
views
Getting motif instances corresponding to regions
homer motif analysis instances regions
updated 5.1 years ago by 35k • written 5.1 years ago by ▴ 120
7
votes
3
replies
4.3k
views
Differences between motif enrichment analysis and footprinting in the context of DNAse-seq/ATAC-seq
footprinting atac-seq dnase-seq motifs
updated 5.1 years ago by 12k • written 5.1 years ago by ▴ 120
10
votes
9
replies
4.3k
views
TPKM vs FPKM
RNA-Seq FPKM
updated 5.5 years ago by 82k • written 5.5 years ago by ▴ 120
3
votes
4
replies
1.7k
views
How to get regions with mapped reads
bed bam RNA-Seq bedtools
updated 13 months ago by 43k • written 5.5 years ago by ▴ 120
5
votes
5
replies
1.7k
views
Ovation RNA-seq system, bionfomatic alignment and htseq-count
RNA-Seq hisat2 htseq-count
updated 5.5 years ago by ★ 1.9k • written 5.5 years ago by ▴ 120
8
votes
8
replies
4.9k
views
Can I convert normalized counts from DESEQ2 into fpkm?
RNA-Seq deseq normalization fpkm
5.7 years ago by nanoide ▴ 120
5
votes
4
replies
3.1k
views
Remove secondary alignments in RNA-seq analysis?
RNA-seq HISAT2 alignment
5.8 years ago by nanoide ▴ 120
0
votes
3
replies
3.5k
views
Doubt using HOMER annotatePeaks.pl
ChIP-Seq HOMER MACS2
updated 2.2 years ago by • 0 • written 5.8 years ago by ▴ 120
4
votes
6
replies
6.7k
views
ATAC-seq macs2 peak calling bampe mode extension shift
ATAC-seq ChIP-Seq macs peaks
updated 5.9 years ago by ▴ 90 • written 5.9 years ago by ▴ 120
27 results • Page 1 of 1
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