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questions
1
vote
2
replies
267
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
9 days ago by
bioinfo
▴ 150
0
votes
0
replies
153
views
How should I make kallisto indexes?
kallisto
updated 10 days ago by
GenoMax
141k • written 10 days ago by
bioinfo
▴ 150
2
votes
2
replies
259
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
10 days ago by
bioinfo
▴ 150
0
votes
1
reply
198
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq
single-cell
scanpy
updated 21 days ago by
Ram
43k • written 21 days ago by
bioinfo
▴ 150
0
votes
5
replies
290
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 21 days ago by
Ram
43k • written 25 days ago by
bioinfo
▴ 150
3
votes
7
replies
484
views
How does kallisto handle multi mapped reads?
kallisto
updated 9 weeks ago by
dsull
★ 5.8k • written 9 weeks ago by
bioinfo
▴ 150
0
votes
2
replies
342
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 8 days ago by
Ehsan
• 0 • written 9 weeks ago by
bioinfo
▴ 150
0
votes
0
replies
281
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
4 months ago by
bioinfo
▴ 150
4
votes
2
replies
610
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq
deseq2
updated 5 months ago by
i.sudbery
19k • written 5 months ago by
bioinfo
▴ 150
3
votes
7
replies
961
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 21 days ago by
Ram
43k • written 5 months ago by
bioinfo
▴ 150
3
votes
4
replies
667
views
Why am I getting different results with kallisto?
kallisto
5 months ago by
bioinfo
▴ 150
2
votes
3
replies
469
views
Are truseq adapter sequences picked up by FASTQC?
fastqc
truseq
updated 5 months ago by
GenoMax
141k • written 5 months ago by
bioinfo
▴ 150
0
votes
0
replies
327
views
How to convert dataframe properly to anndata?
single-cell
python
anndata
updated 21 days ago by
Ram
43k • written 6 months ago by
bioinfo
▴ 150
0
votes
0
replies
324
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python
anndata
atac-seq
updated 21 days ago by
Ram
43k • written 6 months ago by
bioinfo
▴ 150
0
votes
0
replies
299
views
How to subsample ATAC fragment file?
single-cell
atac-seq
scRNA-seq
updated 21 days ago by
Ram
43k • written 6 months ago by
bioinfo
▴ 150
0
votes
2
replies
1.3k
views
Removing constant/zero columns for PCA?
R
pca
updated 6 months ago by
Mensur Dlakic
★ 27k • written 6 months ago by
bioinfo
▴ 150
1
vote
4
replies
679
views
How to assign gene names after kallisto when I add GFP?
tximport
RNA-seq
kallisto
6 months ago by
bioinfo
▴ 150
1
vote
8
replies
1.8k
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq
scanpy
single-cell
7 months ago by
bioinfo
▴ 150
5
votes
2
replies
649
views
How to calculate GC content of reads that mapped to a specific gene?
STAR
RNA-seq
7 months ago by
bioinfo
▴ 150
0
votes
8
replies
890
views
Can the DESeq2 object for paired data be set with design= ~ batch + condition?
rna-seq
deseq2
7 months ago by
bioinfo
▴ 150
1
vote
1
reply
568
views
Do I need to perform basic filtering before using scrublet?
scanpy
scrublet
updated 8 months ago by
GenoMax
141k • written 8 months ago by
bioinfo
▴ 150
0
votes
2
replies
960
views
How to choose threshold for scrublet?
rna-seq
scrublet
8 months ago by
bioinfo
▴ 150
1
vote
5
replies
930
views
Questions about per base sequence quality and GC content.
fastqc
fastq
seq
RNA
8 months ago by
bioinfo
▴ 150
3
votes
3
replies
714
views
How to assign gene names to ensembl IDs if species not in Biomart
biomart
ensembl
8 months ago by
bioinfo
▴ 150
0
votes
4
replies
1.4k
views
Why do I need to sort and index gtf file for IGV?
igv
updated 9 months ago by
ATpoint
82k • written 9 months ago by
bioinfo
▴ 150
3
votes
3
replies
729
views
Where can I find the --chromosomes file for kallisto?
kallisto
updated 9 months ago by
GenoMax
141k • written 9 months ago by
bioinfo
▴ 150
3
votes
2
replies
590
views
How to figure out adapter sequences in RNA seq?
adapters
rna-seq
updated 10 months ago by
rfran010
▴ 900 • written 10 months ago by
bioinfo
▴ 150
1
vote
0
replies
404
views
How does kallisto genomebam handle multi mapping reads?
kallisto
updated 10 months ago by
Ram
43k • written 10 months ago by
bioinfo
▴ 150
4
votes
5
replies
778
views
Does adding reads cause batch effects?
kallisto
RNAseq
10 months ago by
bioinfo
▴ 150
0
votes
0
replies
493
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy
hashtag
hashsolo
RNAseq
12 months ago by
bioinfo
▴ 150
1
vote
3
replies
1.3k
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger.
seq
hashsolo
rna
12 months ago by
bioinfo
▴ 150
0
votes
2
replies
622
views
Do I need to specify the introns on the gtf file for cellranger?
fasta
gtf
cellranger
scRNAseq
updated 12 months ago by
GenoMax
141k • written 12 months ago by
bioinfo
▴ 150
2
votes
1
reply
623
views
Can I normalize several samples with DESeq2 and then do pairwise comparisons?
deseq2
rna-seq
updated 12 months ago by
rpolicastro
13k • written 12 months ago by
bioinfo
▴ 150
1
vote
1
reply
569
views
Do indexes made with cDNA fasta file contain only mRNAs?
ensembl
kallisto
updated 13 months ago by
dsull
★ 5.8k • written 13 months ago by
bioinfo
▴ 150
0
votes
0
replies
366
views
How to analyze SCRNA seq data labelled with LARRY?
single
lineage
RNA
tracing
LARRY
updated 13 months ago by
GenoMax
141k • written 13 months ago by
bioinfo
▴ 150
2
votes
5
replies
1.4k
views
How to add gene entry to gtf file?
single-cell
cellranger
updated 14 months ago by
Ram
43k • written 14 months ago by
bioinfo
▴ 150
2
votes
5
replies
1.1k
views
Problem with tximport and plasmodium falciparum
tximport
14 months ago by
bioinfo
▴ 150
1
vote
3
replies
2.0k
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
14 months ago by
bioinfo
▴ 150
1
vote
5
replies
1.2k
views
How to interpret dotplot from enrichment analysis with gseapy?
gsea
single-cell
gseapy
enrichR
14 months ago by
bioinfo
▴ 150
3
votes
4
replies
816
views
How to remove a gene before making a cellranger reference?
fasta
gtf
cellranger
scRNAseq
updated 14 months ago by
ATpoint
82k • written 14 months ago by
bioinfo
▴ 150
1
vote
2
replies
489
views
Do I need to merge files after downloading them from SRA?
rna-seq
sra
14 months ago by
bioinfo
▴ 150
14
votes
8
replies
4.7k
views
Encountering error when loading scanpy?
scanpy
single-cell
scRNA-seq
14 months ago by
bioinfo
▴ 150
1
vote
0
replies
446
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
14 months ago by
bioinfo
▴ 150
3
votes
2
replies
560
views
Do I need to correct for sequencing depth in bulk RNA seq?
kallisto
RNA-seq
updated 14 months ago by
Ram
43k • written 15 months ago by
bioinfo
▴ 150
0
votes
0
replies
497
views
How to adjust graph in scanpy?
scanpy
single-cell
RNA-seq
15 months ago by
bioinfo
▴ 150
0
votes
0
replies
664
views
How to analyze scRNA seq data with time points (Seurat/Pseudotime)?
monocle3
scRNA-seq
pseudotime
Seurat
R
15 months ago by
bioinfo
▴ 150
2
votes
2
replies
1.1k
views
How to perform scRNA seq analysis?
single-cell
pseudobulk
seurat
15 months ago by
bioinfo
▴ 150
3
votes
2
replies
781
views
Does the bootstrap in kallisto affect the BAM files?
RNAseq
kallisto
BAM
16 months ago by
bioinfo
▴ 150
1
vote
4
replies
1.4k
views
Issues with chromosome file in kallisto
kallisto
updated 16 months ago by
dsull
★ 5.8k • written 16 months ago by
bioinfo
▴ 150
1
vote
2
replies
835
views
How to run UMAP on single cell results from 2 different runs?
single-cell
seurat
cellranger
updated 16 months ago by
LChart
3.9k • written 16 months ago by
bioinfo
▴ 150
68 results • Page
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