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Showing :
questions
4
votes
4
replies
297
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 6 days ago by
ATpoint
72k • written 6 days ago by
bioinfo
▴ 80
0
votes
0
replies
179
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy
hashtag
hashsolo
RNAseq
6 weeks ago by
bioinfo
▴ 80
1
vote
3
replies
479
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger.
seq
hashsolo
rna
6 weeks ago by
bioinfo
▴ 80
0
votes
2
replies
243
views
Do I need to specify the introns on the gtf file for cellranger?
fasta
gtf
cellranger
scRNAseq
updated 7 weeks ago by
GenoMax
130k • written 7 weeks ago by
bioinfo
▴ 80
2
votes
1
reply
256
views
Can I normalize several samples with DESeq2 and then do pairwise comparisons?
deseq2
rna-seq
updated 8 weeks ago by
rpolicastro
12k • written 8 weeks ago by
bioinfo
▴ 80
1
vote
1
reply
243
views
Do indexes made with cDNA fasta file contain only mRNAs?
ensembl
kallisto
updated 3 months ago by
dsull
★ 4.2k • written 3 months ago by
bioinfo
▴ 80
0
votes
0
replies
212
views
How to analyze SCRNA seq data labelled with LARRY?
single
lineage
RNA
tracing
LARRY
updated 3 months ago by
GenoMax
130k • written 3 months ago by
bioinfo
▴ 80
2
votes
5
replies
624
views
How to add gene entry to gtf file?
single-cell
cellranger
updated 3 months ago by
Ram
39k • written 3 months ago by
bioinfo
▴ 80
2
votes
5
replies
676
views
Problem with tximport and plasmodium falciparum
tximport
3 months ago by
bioinfo
▴ 80
1
vote
3
replies
933
views
How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?
single-cell
scanpy
RNA-seq
UMAP
3 months ago by
bioinfo
▴ 80
1
vote
5
replies
560
views
How to interpret dotplot from enrichment analysis with gseapy?
gsea
single-cell
gseapy
enrichR
3 months ago by
bioinfo
▴ 80
3
votes
4
replies
454
views
How to remove a gene before making a cellranger reference?
fasta
gtf
cellranger
scRNAseq
updated 3 months ago by
ATpoint
72k • written 3 months ago by
bioinfo
▴ 80
1
vote
2
replies
258
views
Do I need to merge files after downloading them from SRA?
rna-seq
sra
3 months ago by
bioinfo
▴ 80
11
votes
8
replies
1.5k
views
Encountering error when loading scanpy?
scanpy
single-cell
scRNA-seq
3 months ago by
bioinfo
▴ 80
0
votes
0
replies
227
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
4 months ago by
bioinfo
▴ 80
3
votes
2
replies
328
views
Do I need to correct for sequencing depth in bulk RNA seq?
kallisto
RNA-seq
updated 3 months ago by
Ram
39k • written 4 months ago by
bioinfo
▴ 80
0
votes
0
replies
217
views
How to adjust graph in scanpy?
scanpy
single-cell
RNA-seq
4 months ago by
bioinfo
▴ 80
0
votes
0
replies
342
views
How to analyze scRNA seq data with time points (Seurat/Pseudotime)?
monocle3
scRNA-seq
pseudotime
Seurat
R
4 months ago by
bioinfo
▴ 80
2
votes
2
replies
561
views
How to perform scRNA seq analysis?
single-cell
pseudobulk
seurat
5 months ago by
bioinfo
▴ 80
3
votes
2
replies
557
views
Does the bootstrap in kallisto affect the BAM files?
RNAseq
kallisto
BAM
5 months ago by
bioinfo
▴ 80
1
vote
4
replies
901
views
Issues with chromosome file in kallisto
kallisto
updated 5 months ago by
dsull
★ 4.2k • written 5 months ago by
bioinfo
▴ 80
1
vote
2
replies
376
views
How to run UMAP on single cell results from 2 different runs?
single-cell
seurat
cellranger
updated 6 months ago by
LChart
2.6k • written 6 months ago by
bioinfo
▴ 80
1
vote
3
replies
378
views
How to check gene properties (eg GC, repetitiveness, average expression level)?
deseq2
kallisto
RNA-seq
updated 3 months ago by
Ram
39k • written 6 months ago by
bioinfo
▴ 80
0
votes
10
replies
606
views
Can I demultiplex run based on i5 sequence?
demultiplexing
bcl2fastq
updated 6 months ago by
GenoMax
130k • written 6 months ago by
bioinfo
▴ 80
3
votes
13
replies
1.7k
views
How to choose parameters for kallisto single end mode?
kallisto
RNA-seq
updated 25 days ago by
Istvan Albert
98k • written 7 months ago by
bioinfo
▴ 80
7
votes
3
replies
974
views
Should I merge my technical replicates for bulk RNA seq?
RNA-seq
DESeq2
updated 3 months ago by
Ram
39k • written 7 months ago by
bioinfo
▴ 80
4
votes
4
replies
551
views
Can I perform DE analysis with Seurat if I only have one sample per condition?
single
RNA
Seq
cell
seurat
updated 7 months ago by
LChart
2.6k • written 7 months ago by
bioinfo
▴ 80
0
votes
0
replies
200
views
How do I get estimated gene counts for a reference that contains GFP using Kallisto?
gene
ensembl
tximport
kallisto
8 months ago by
bioinfo
▴ 80
4
votes
4
replies
749
views
How can I confirm that I installed bcl2fastq correctly?
bcl2fastq
linux
ubuntu
9 months ago by
bioinfo
▴ 80
3
votes
2
replies
456
views
Why do I get a positive gene expression with qPCR for one my genes but in with when doing bulk RNA seq I get a count of 0?
gene
qpcr
kallisto
seq
expression
rna
updated 10 months ago by
dsull
★ 4.2k • written 10 months ago by
bioinfo
▴ 80
1
vote
3
replies
509
views
How to filter .fa file by gene_biotype
rna-seq
kallisto
updated 11 months ago by
Ram
39k • written 12 months ago by
bioinfo
▴ 80
0
votes
7
replies
742
views
6 follow
How to create kallisto index that does not include ribosomal genes
enseml
kallisto
RNA-seq
updated 5 months ago by
Ram
39k • written 12 months ago by
bioinfo
▴ 80
0
votes
0
replies
264
views
Replicates in sc-RNA seq have different amount of cells-Can I still use them for the analysis?
Cell
seurat
Single
updated 12 months ago by
ATpoint
72k • written 12 months ago by
bioinfo
▴ 80
2
votes
4
replies
697
views
Can I use the transcripts_to_genes.txt file from kallisto for bulk RNA seq data?
kallisto
updated 13 months ago by
Ram
39k • written 13 months ago by
bioinfo
▴ 80
2
votes
3
replies
686
views
Ensembl version for mapping and annotating genes
rna-seq
kallisto
updated 11 months ago by
Ram
39k • written 13 months ago by
bioinfo
▴ 80
6
votes
2
replies
404
views
Ensembl version
ensembl
kallisto
updated 5 months ago by
Ram
39k • written 13 months ago by
bioinfo
▴ 80
2
votes
2
replies
1.6k
views
Cellranger command for RNA velocity
cellranger
Cell
velocity
RNA
Single
updated 16 months ago by
Friederike
8.7k • written 16 months ago by
bioinfo
▴ 80
4
votes
2
replies
702
views
Estimated gene counts with tximport
RNA-seq
ensembl
tximport
kallisto
updated 11 months ago by
Ram
39k • written 17 months ago by
bioinfo
▴ 80
3
votes
3
replies
1.1k
views
Will Kallisto show a decrease in the TPM value if I have knocked out 2 of the 8 exons from a gene?
RNA-seq
updated 11 months ago by
Ram
39k • written 18 months ago by
bioinfo
▴ 80
2
votes
2
replies
922
views
How to demultiplex a single indexed library on a dual indexed flow cell?
Cell
Single
updated 18 months ago by
GenoMax
130k • written 18 months ago by
bioinfo
▴ 80
40 results • Page
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