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questions
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 16 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
6
votes
2
replies
355
views
How I should set `STAR` parameters to keep all the intronic reads?
STAR
mapping
updated 8 weeks ago by
dsull
★ 5.8k • written 8 weeks ago by
Dan
▴ 180
6
votes
8
replies
1.0k
views
The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
RNA-velocity
updated 6 months ago by
james.hawley
▴ 40 • written 6 months ago by
Dan
▴ 180
8
votes
5
replies
888
views
Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATAC data analysis?
multiome
single-cell
updated 7 months ago by
ATpoint
82k • written 7 months ago by
Dan
▴ 180
3
votes
1
reply
518
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq
ATAC-seq
updated 9 months ago by
Papyrus
★ 2.9k • written 9 months ago by
Dan
▴ 180
6
votes
5
replies
2.5k
views
umap failed to cluster the cells
single-cell
umap
9 months ago by
Dan
▴ 180
1
vote
0
replies
332
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
10 months ago by
Dan
▴ 180
2
votes
2
replies
603
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap
deepTools
10 months ago by
Dan
▴ 180
8
votes
9
replies
2.5k
views
Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st intron, ..., 3'UTR, intergenic, ...`
BAM
11 months ago by
Dan
▴ 180
1
vote
2
replies
478
views
`MOFAobject@expectations` is empty list
MOFA2
updated 11 months ago by
Ram
43k • written 11 months ago by
Dan
▴ 180
4
votes
3
replies
727
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
11 months ago by
Dan
▴ 180
0
votes
0
replies
441
views
How to save the digital percentage of `ChIPseeker::plotAnnoPie()` to a table?
ChIPseeker
12 months ago by
Dan
▴ 180
3
votes
0
replies
350
views
How to calculate the false discovery proportion from the p-value histogram?
false-discovery-rate
12 months ago by
Dan
▴ 180
1
vote
0
replies
630
views
What is the difference between `possorted_genome_bam.bam` in the output of `cellranger count` and `sample_alignments.bam` in the output of `cellrange…
single-cell
analysis
RNA-seq
velocity
12 months ago by
Dan
▴ 180
5
votes
1
reply
546
views
How to derive conditional maximum likelihood of the sum of independent negative binomial variables?
limma
voom
biostatistics
13 months ago by
Dan
▴ 180
3
votes
2
replies
504
views
How to quantify the reads of each peak for ChIP-seq data?
ChIP-seq
DiffBind
14 months ago by
Dan
▴ 180
3
votes
2
replies
561
views
How to find all of the new RNA splices from bulk RNA-seq data?
RNA-seq
RNA-splices
updated 14 months ago by
dthorbur
★ 1.9k • written 14 months ago by
Dan
▴ 180
4
votes
2
replies
660
views
How to quantify the reads of peaks?
ChIP-seq
ATAC-seq
updated 14 months ago by
heritabilities
▴ 20 • written 14 months ago by
Dan
▴ 180
4
votes
3
replies
779
views
Is there a package that can do downstream analysis of single-cell V(D)J sequencing?
single-cell-VDJ
14 months ago by
Dan
▴ 180
1
vote
3
replies
643
views
How to do Binding and Expression Target Analysis?
ChIP-seq
updated 14 months ago by
Ram
43k • written 14 months ago by
Dan
▴ 180
6
votes
4
replies
1.0k
views
How to install `BETA` on linux server?
ChIP-seq
BETA
updated 14 months ago by
ATpoint
82k • written 14 months ago by
Dan
▴ 180
8
votes
7
replies
1.1k
views
6 follow
How should I deduce the variance and expectation of the logarithm of a variable in the `voom` paper?
Biostatistics
voom
limma
14 months ago by
Dan
▴ 180
2
votes
1
reply
504
views
How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using `deepTools`?
deepTools
updated 14 months ago by
Trivas
★ 1.7k • written 14 months ago by
Dan
▴ 180
2
votes
3
replies
717
views
Is there a method to group and summarize the `homer` `findMotifsGenome.pl` output?
Motif-analysis
15 months ago by
Dan
▴ 180
0
votes
0
replies
407
views
How to customize the Profile values of `plotHeatmap` of `deeptools`?
deeptools
15 months ago by
Dan
▴ 180
2
votes
1
reply
911
views
How can I customize `plotheatmap` of `deepTools` to different colors for different `.bed` file regions and how to customize the color of the intensit…
deepTools
plotheatmap
updated 18 months ago by
M.O.L.S
▴ 100 • written 19 months ago by
Dan
▴ 180
6
votes
4
replies
1.7k
views
What is the best practice for the analysis of single-cell RNA-seq of mouse and human mixed cells?
single-cell
RNA-seq
19 months ago by
Dan
▴ 180
3
votes
10
replies
1.1k
views
Can I directly compare the regions defined by peaks from pair-end 50 and pair-end 100 ATAC-seq?
ATAC-seq
updated 19 months ago by
ATpoint
82k • written 19 months ago by
Dan
▴ 180
5
votes
5
replies
1.5k
views
How to normalize the intensity of bigwig files based on a group of house-keeping genes in ATAC-seq data?
ATAC
bigwig
updated 20 months ago by
ATpoint
82k • written 20 months ago by
Dan
▴ 180
5
votes
3
replies
878
views
How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
awk
updated 20 months ago by
LChart
3.9k • written 20 months ago by
Dan
▴ 180
3
votes
1
reply
505
views
How to change the chromosome names of the head line of fasta file?
sed
updated 21 months ago by
ATpoint
82k • written 21 months ago by
Dan
▴ 180
14
votes
5
replies
1.7k
views
nextflow error
nextflow
21 months ago by
Dan
▴ 180
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 20 hours ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
4
votes
1
reply
551
views
How to define the open chromatin region in ATACseq? And how to filter the .bam file based on insert size?
ATAC
updated 22 months ago by
ATpoint
82k • written 22 months ago by
Dan
▴ 180
2
votes
2
replies
667
views
It is weird there are no reads less than 100 bp in qualimap.
qualimap
22 months ago by
Dan
▴ 180
4
votes
3
replies
823
views
why bowtie2 doesn’t report longer than 500bp inserts?
bowtie2
BAM
updated 22 months ago by
acvill
▴ 340 • written 22 months ago by
Dan
▴ 180
3
votes
2
replies
491
views
Is it possible to subsample the especially large files during alignment using Bowtie2 or bwa?
bwa
Bowtie2
updated 22 months ago by
GenoMax
141k • written 22 months ago by
Dan
▴ 180
0
votes
0
replies
318
views
How to choose the library normalization size in single cell RNA-seq data Preprocessing?
cell
single
RNA-seq
2.1 years ago by
Dan
▴ 180
0
votes
2
replies
1.2k
views
Can I change the mouse symbol gene name to upper case to run GSEA using gmt files that contain upper case gene names?
GSEA
gmt
2.1 years ago by
Dan
▴ 180
6
votes
2
replies
839
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 10 months ago by
Ram
43k • written 2.2 years ago by
Dan
▴ 180
0
votes
0
replies
629
views
How to analyze whole-genome data using Picard and GATK?
whole-genome
GATK
Picard
2.4 years ago by
Dan
▴ 180
3
votes
2
replies
1.2k
views
Which is @RG read group in the head of bam files?
sam
bam
2.4 years ago by
Dan
▴ 180
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