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questions
0
votes
8
replies
5.4k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 5 weeks ago by
EricYang
• 0 • written 4.8 years ago by
Dan
▴ 180
6
votes
2
replies
395
views
How I should set `STAR` parameters to keep all the intronic reads?
STAR
mapping
updated 11 weeks ago by
dsull
★ 6.0k • written 11 weeks ago by
Dan
▴ 180
6
votes
8
replies
1.1k
views
The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
RNA-velocity
updated 7 months ago by
james.hawley
▴ 40 • written 7 months ago by
Dan
▴ 180
8
votes
5
replies
937
views
Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATAC data analysis?
multiome
single-cell
updated 8 months ago by
ATpoint
82k • written 8 months ago by
Dan
▴ 180
3
votes
1
reply
541
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq
ATAC-seq
updated 10 months ago by
Papyrus
★ 2.9k • written 10 months ago by
Dan
▴ 180
6
votes
5
replies
2.6k
views
umap failed to cluster the cells
single-cell
umap
10 months ago by
Dan
▴ 180
1
vote
0
replies
344
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
11 months ago by
Dan
▴ 180
2
votes
2
replies
647
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap
deepTools
11 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
12 months ago by
Dan
▴ 180
1
vote
2
replies
501
views
`MOFAobject@expectations` is empty list
MOFA2
updated 12 months ago by
Ram
43k • written 12 months ago by
Dan
▴ 180
4
votes
3
replies
756
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
12 months ago by
Dan
▴ 180
0
votes
0
replies
456
views
How to save the digital percentage of `ChIPseeker::plotAnnoPie()` to a table?
ChIPseeker
13 months ago by
Dan
▴ 180
3
votes
0
replies
356
views
How to calculate the false discovery proportion from the p-value histogram?
false-discovery-rate
13 months ago by
Dan
▴ 180
1
vote
0
replies
645
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
13 months ago by
Dan
▴ 180
5
votes
1
reply
565
views
How to derive conditional maximum likelihood of the sum of independent negative binomial variables?
limma
voom
biostatistics
14 months ago by
Dan
▴ 180
3
votes
2
replies
521
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
580
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
★ 2.0k • written 14 months ago by
Dan
▴ 180
4
votes
2
replies
683
views
How to quantify the reads of peaks?
ChIP-seq
ATAC-seq
updated 14 months ago by
heritabilities
▴ 20 • written 15 months ago by
Dan
▴ 180
4
votes
3
replies
803
views
Is there a package that can do downstream analysis of single-cell V(D)J sequencing?
single-cell-VDJ
15 months ago by
Dan
▴ 180
1
vote
3
replies
666
views
How to do Binding and Expression Target Analysis?
ChIP-seq
updated 15 months ago by
Ram
43k • written 15 months ago by
Dan
▴ 180
6
votes
4
replies
1.0k
views
How to install `BETA` on linux server?
ChIP-seq
BETA
updated 15 months ago by
ATpoint
82k • written 15 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
15 months ago by
Dan
▴ 180
2
votes
1
reply
523
views
How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using `deepTools`?
deepTools
updated 15 months ago by
Trivas
★ 1.8k • written 15 months ago by
Dan
▴ 180
2
votes
3
replies
739
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
414
views
How to customize the Profile values of `plotHeatmap` of `deeptools`?
deeptools
16 months ago by
Dan
▴ 180
2
votes
1
reply
933
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
1.8k
views
What is the best practice for the analysis of single-cell RNA-seq of mouse and human mixed cells?
single-cell
RNA-seq
20 months ago by
Dan
▴ 180
3
votes
10
replies
1.2k
views
Can I directly compare the regions defined by peaks from pair-end 50 and pair-end 100 ATAC-seq?
ATAC-seq
updated 20 months ago by
ATpoint
82k • written 20 months ago by
Dan
▴ 180
5
votes
5
replies
1.6k
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
901
views
How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
awk
updated 21 months ago by
LChart
3.9k • written 21 months ago by
Dan
▴ 180
3
votes
1
reply
523
views
How to change the chromosome names of the head line of fasta file?
sed
updated 22 months ago by
ATpoint
82k • written 22 months ago by
Dan
▴ 180
14
votes
5
replies
1.8k
views
nextflow error
nextflow
22 months ago by
Dan
▴ 180
3
votes
3
replies
2.5k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 24 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
4
votes
1
reply
562
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
680
views
It is weird there are no reads less than 100 bp in qualimap.
qualimap
23 months ago by
Dan
▴ 180
4
votes
3
replies
845
views
why bowtie2 doesn’t report longer than 500bp inserts?
bowtie2
BAM
updated 23 months ago by
acvill
▴ 340 • written 23 months ago by
Dan
▴ 180
3
votes
2
replies
504
views
Is it possible to subsample the especially large files during alignment using Bowtie2 or bwa?
bwa
Bowtie2
updated 23 months ago by
GenoMax
142k • written 23 months ago by
Dan
▴ 180
0
votes
0
replies
328
views
How to choose the library normalization size in single cell RNA-seq data Preprocessing?
cell
single
RNA-seq
2.2 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
2.2 years ago by
Dan
▴ 180
6
votes
2
replies
859
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 11 months ago by
Ram
43k • written 2.2 years ago by
Dan
▴ 180
0
votes
0
replies
647
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
1.3k
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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