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3
votes
2
replies
389
views
DESeq2 outliers-should I be concerned?
deseq2
updated 5 days ago by 88k • written 7 days ago by ▴ 150
0
votes
2
replies
349
views
Kallisto to tximport to deseq2
enseml deseq2 Kallisto
updated 13 days ago by 151k • written 13 days ago by ▴ 150
0
votes
2
replies
338
views
Question about assigning gene names, tximport and DESeq2
tximport deseq2
6 weeks ago by bioinfo ▴ 150
1
vote
3
replies
1.7k
views
How to use harmony with scanpy?
scanpy harmony
updated 12 weeks ago by • 0 • written 3 months ago by ▴ 150
2
votes
2
replies
560
views
Should I not have any adapters after trimming?
RNA-seq
updated 3 months ago by 14k • written 3 months ago by ▴ 150
0
votes
0
replies
312
views
Does the order of HTOs matter?
hashsolo scanpy
4 months ago by bioinfo ▴ 150
0
votes
0
replies
278
views
Regression and scaling in scanpy
scanpy
5 months ago by bioinfo ▴ 150
0
votes
1
reply
812
views
When should I normalize and subset adata objects in scanpy?
scanpy scRNA-seq single-cell
updated 9 months ago by 4.9k • written 9 months ago by ▴ 150
2
votes
1
reply
541
views
How to choose cells that co-express several genes with scanpy?
scanpy scRNA-seq single-cell
updated 10 months ago by 4.9k • written 10 months ago by ▴ 150
0
votes
0
replies
312
views
How to run trajectory analysis with only one cell type using palantir?
palantir scanpy
10 months ago by bioinfo ▴ 150
2
votes
1
reply
566
views
Do I need to remove doublets after before or after running hashsolo?
hashsolo scanpy scrublet
updated 10 months ago by ▴ 940 • written 10 months ago by ▴ 150
0
votes
2
replies
570
views
How can I import an unindexed human gtf file in IGV?
igv
10 months ago by bioinfo ▴ 150
0
votes
6
replies
1.0k
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto ensembl
11 months ago by bioinfo ▴ 150
1
vote
3
replies
750
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq trimmomatic
updated 12 months ago by 151k • written 12 months ago by ▴ 150
2
votes
3
replies
816
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart RNAseq kallisto
7 months ago by bioinfo ▴ 150
1
vote
5
replies
1.8k
views
How should I make kallisto indexes?
kallisto
updated 13 months ago by ★ 7.6k • written 13 months ago by ▴ 150
1
vote
2
replies
682
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq kallisto
13 months ago by bioinfo ▴ 150
2
votes
2
replies
854
views
How to row normalize a matrixplot?
scRNA-seq RNA-seq single-cell scanpy
13 months ago by bioinfo ▴ 150
0
votes
1
reply
1.1k
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq single-cell scanpy
updated 13 months ago by 45k • written 13 months ago by ▴ 150
0
votes
5
replies
947
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 13 months ago by 45k • written 13 months ago by ▴ 150
3
votes
7
replies
1.4k
views
How does kallisto handle multi mapped reads?
kallisto
updated 15 months ago by ★ 7.6k • written 15 months ago by ▴ 150
0
votes
2
replies
937
views
How to add motifs in cellranger-arc reference?
gtf scRNAseq fasta cellranger
updated 13 months ago by • 0 • written 15 months ago by ▴ 150
0
votes
0
replies
568
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart kegg deseq2
18 months ago by bioinfo ▴ 150
4
votes
2
replies
1.1k
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq deseq2
updated 18 months ago by 21k • written 18 months ago by ▴ 150
3
votes
7
replies
1.8k
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq illumina adapters
updated 13 months ago by 45k • written 18 months ago by ▴ 150
3
votes
4
replies
1.3k
views
Why am I getting different results with kallisto?
kallisto
18 months ago by bioinfo ▴ 150
2
votes
3
replies
985
views
Are truseq adapter sequences picked up by FASTQC?
fastqc truseq
updated 18 months ago by 151k • written 18 months ago by ▴ 150
0
votes
0
replies
636
views
How to convert dataframe properly to anndata?
single-cell python anndata
updated 13 months ago by 45k • written 19 months ago by ▴ 150
0
votes
0
replies
584
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python anndata atac-seq
updated 13 months ago by 45k • written 19 months ago by ▴ 150
0
votes
0
replies
531
views
How to subsample ATAC fragment file?
single-cell atac-seq scRNA-seq
updated 13 months ago by 45k • written 19 months ago by ▴ 150
0
votes
2
replies
3.3k
views
Removing constant/zero columns for PCA?
R pca
updated 19 months ago by ★ 29k • written 19 months ago by ▴ 150
1
vote
4
replies
1.4k
views
How to assign gene names after kallisto when I add GFP?
tximport RNA-seq kallisto
19 months ago by bioinfo ▴ 150
1
vote
8
replies
4.9k
views
How to plot proportion of cells in each cluster with scanpy?
scRNA-seq scanpy single-cell
20 months ago by bioinfo ▴ 150
5
votes
2
replies
1.1k
views
How to calculate GC content of reads that mapped to a specific gene?
STAR RNA-seq
20 months ago by bioinfo ▴ 150
0
votes
8
replies
1.5k
views
Can the DESeq2 object for paired data be set with design= ~ batch + condition?
rna-seq deseq2
21 months ago by bioinfo ▴ 150
1
vote
1
reply
1.1k
views
Do I need to perform basic filtering before using scrublet?
scanpy scrublet
updated 21 months ago by 151k • written 21 months ago by ▴ 150
0
votes
2
replies
2.1k
views
How to choose threshold for scrublet?
rna-seq scrublet
21 months ago by bioinfo ▴ 150
1
vote
5
replies
1.9k
views
Questions about per base sequence quality and GC content.
fastqc fastq seq RNA
21 months ago by bioinfo ▴ 150
3
votes
3
replies
1.2k
views
How to assign gene names to ensembl IDs if species not in Biomart
biomart ensembl
21 months ago by bioinfo ▴ 150
0
votes
4
replies
4.1k
views
Why do I need to sort and index gtf file for IGV?
igv
updated 22 months ago by 88k • written 22 months ago by ▴ 150
3
votes
3
replies
1.1k
views
Where can I find the --chromosomes file for kallisto?
kallisto
updated 22 months ago by 151k • written 22 months ago by ▴ 150
3
votes
2
replies
1.0k
views
How to figure out adapter sequences in RNA seq?
adapters rna-seq
updated 23 months ago by ★ 1.5k • written 23 months ago by ▴ 150
1
vote
0
replies
569
views
How does kallisto genomebam handle multi mapping reads?
kallisto
updated 23 months ago by 45k • written 23 months ago by ▴ 150
4
votes
5
replies
1.3k
views
Does adding reads cause batch effects?
kallisto RNAseq
23 months ago by bioinfo ▴ 150
0
votes
0
replies
745
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy hashtag hashsolo RNAseq
2.1 years ago by bioinfo ▴ 150
1
vote
3
replies
2.1k
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger. seq hashsolo rna
2.1 years ago by bioinfo ▴ 150
0
votes
2
replies
929
views
Do I need to specify the introns on the gtf file for cellranger?
fasta gtf cellranger scRNAseq
updated 2.1 years ago by 151k • written 2.1 years ago by ▴ 150
3
votes
1
reply
885
views
Can I normalize several samples with DESeq2 and then do pairwise comparisons?
deseq2 rna-seq
updated 2.1 years ago by 13k • written 2.1 years ago by ▴ 150
1
vote
1
reply
815
views
Do indexes made with cDNA fasta file contain only mRNAs?
ensembl kallisto
updated 2.2 years ago by ★ 7.6k • written 2.2 years ago by ▴ 150
0
votes
0
replies
525
views
How to analyze SCRNA seq data labelled with LARRY?
single lineage RNA tracing LARRY
updated 2.2 years ago by 151k • written 2.2 years ago by ▴ 150
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