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308 results • Page
1 of 7
Sort: Votes
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Views
Votes
Replies
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 5 days ago by
Ram
40k • written 24 months ago by
A_heath
▴ 140
5
votes
7
replies
416
views
Salmon index not progressing
salmon
updated 4 days ago by
Michael
53k • written 5 days ago by
camillab.
▴ 130
5
votes
4
replies
269
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
1 day ago by
Mehwish
• 0
5
votes
3
replies
281
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 12 days ago by
Ram
40k • written 12 days ago by
sarahmanderni
▴ 90
4
votes
3
replies
388
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
25 days ago by
stefano.iantorno
▴ 70
4
votes
2
replies
428
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 6 days ago by
yhdist
▴ 70 • written 9 days ago by
Cookin
▴ 10
4
votes
5
replies
487
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
8 days ago by
psm
▴ 100
3
votes
4
replies
317
views
Visualization of multiple sequence alignment quality
blastp
blast
msa
updated 21 days ago by
GenoMax
134k • written 21 days ago by
dec986
▴ 370
3
votes
4
replies
425
views
During alignment STAR has stopped at started alignment step
STAR
updated 7 days ago by
Ram
40k • written 6 weeks ago by
Santhi
• 0
3
votes
3
replies
2.2k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 4 hours ago by
Ram
40k • written 2.0 years ago by
Anand
▴ 40
3
votes
2
replies
150
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 13 hours ago by
Basti
★ 1.7k • written 1 day ago by
epianalysis
• 0
3
votes
5
replies
394
views
Ensembl site unresponsive in clusterProfiler analyses
parallell
clusterProfiler
R
updated 19 days ago by
manaswwm
▴ 440 • written 21 days ago by
enanoide
• 0
3
votes
5
replies
439
views
Optimal number of features to use when integrate multi samples by Seurat in scRNAseq
scRNASeq
Seurat
updated 25 days ago by
Ram
40k • written 25 days ago by
alwayshope
▴ 30
3
votes
10
replies
496
views
STAR index not working
STAR
RNA-Seq
5 days ago by
camillab.
▴ 130
3
votes
5
replies
523
views
Neither pysam nor samtools reading HTTPS-sourced BAM file correctly
bam
pysam
samtools
updated 23 days ago by
Istvan Albert
98k • written 25 days ago by
Alex Reynolds
35k
3
votes
4
replies
358
views
Weighted analysis
RNA-seq
8 days ago by
Peter
• 0
3
votes
5
replies
1.0k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio
purge_dups
Assembly
bionano
updated 12 days ago by
colindaven
5.5k • written 2.6 years ago by
pablo
▴ 280
2
votes
1
reply
175
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV
WES
updated 8 days ago by
Pierre Lindenbaum
157k • written 8 days ago by
Nadav
▴ 10
2
votes
0
replies
140
views
the dispersion estimation of edgeR and DESeq2
estimation
dipersion
edgeR
DESeq2
7 days ago by
tommy
▴ 30
2
votes
3
replies
278
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 6 days ago by
Ram
40k • written 6 days ago by
txema.heredia
▴ 80
2
votes
2
replies
355
views
Currently lost between contigs, scaffolds and chromosomes due to positionally sorted scRNAseq bam files
bam
contigs
scRNAseq
updated 21 days ago by
ATpoint
76k • written 21 days ago by
nyxtoviopouli
• 0
2
votes
13
replies
1.5k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 4 hours ago by
Ram
40k • written 5 weeks ago by
epianalysis
• 0
2
votes
2
replies
265
views
Pangenome using Orthofinder
OrthoFinder
Pangenome
bacteria
8 days ago by
kirankumareripogu
▴ 10
2
votes
3
replies
289
views
Genewise output help
genewise
updated 7 days ago by
Jean-Karim Heriche
26k • written 8 days ago by
lorenzoedg
• 0
2
votes
4
replies
434
views
Help with celltype annotation
seurat
single-cell
10 days ago by
Chris
▴ 180
2
votes
2
replies
215
views
Clustering algorithm based on grouping sequences into gene families
gene-families
clustering
updated 8 days ago by
Ram
40k • written 9 days ago by
francesco
• 0
2
votes
5
replies
453
views
Dowload data from password protected cloud storage
data-transfer
wget
rclone
updated 18 days ago by
Joe
21k • written 19 days ago by
Paula
▴ 60
2
votes
9
replies
401
views
Calculation of TMB on gene level
genomics
updated 8 hours ago by
svp
▴ 590 • written 1 day ago by
smrutimayipanda
▴ 20
2
votes
7
replies
683
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph
reads
pangenome
vg
paired-end
22 days ago by
nkls063408
• 0
2
votes
4
replies
313
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 6 days ago by
Ram
40k • written 6 days ago by
P
• 0
2
votes
3
replies
340
views
How to label only a few genes of interest in heatmap of bulk RNA-seq
RNA-seq
updated 19 days ago by
Ram
40k • written 21 days ago by
Chris
▴ 180
2
votes
5
replies
299
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 4 hours ago by
rfran010
▴ 800 • written 3 days ago by
Athena
• 0
2
votes
4
replies
374
views
join the control replicates
RNA-seq
updated 11 days ago by
seidel
11k • written 12 days ago by
Jean Pierre
• 0
2
votes
4
replies
241
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
1 day ago by
camillab.
▴ 130
2
votes
4
replies
273
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
2 days ago by
Grace
• 0
2
votes
20
replies
1.5k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
19 days ago by
Maxine
▴ 30
2
votes
5
replies
365
views
Cluster annotation in single cell
Single-cell
updated 20 days ago by
Ram
40k • written 20 days ago by
synat.keam
▴ 80
2
votes
3
replies
1.5k
views
Racon command line with paired-ends Illumina reads
Illumina
Racon
updated 5 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
2
votes
5
replies
390
views
Centrality analysis to identify TFs
TF
updated 25 days ago by
biofalconch
▴ 980 • written 27 days ago by
Chris
▴ 180
1
vote
1
reply
730
views
GO enrichment and KEGG output empty
enrichment
GO
KEGG
clusterprofiler
NCBI
updated 28 days ago by
cardon.chc
• 0 • written 24 months ago by
estpallag
▴ 10
1
vote
2
replies
284
views
functional analysis prediction
functionalanalysis
metabarcoding
16S
8 days ago by
safeassli
• 0
1
vote
4
replies
313
views
htseq-count reports count values for deleted genes
rna-seq
htseq
15 days ago by
kmyers2
▴ 80
1
vote
1
reply
246
views
Bioconductor Package Installation
bioconductor
updated 12 days ago by
Ram
40k • written 12 days ago by
oduduabasi.isaiah
• 0
1
vote
2
replies
138
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
1 day ago by
alwayshope
▴ 30
1
vote
5
replies
667
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 5 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
1
vote
2
replies
272
views
Dotplot error: subscript out of bound
R
scRNA-seq
seurat
2 days ago by
Xuhao
• 0
1
vote
5
replies
165
views
How the first sequencing template removed in pair end sequencing
NGS
RNA-seq
WGS
sequence
3 hours ago by
octpus616
▴ 80
1
vote
2
replies
221
views
Problem with Mageck paired analysis
Mageck
updated 15 days ago by
Meisam
▴ 200 • written 15 days ago by
toma.85
• 0
1
vote
5
replies
347
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 13 hours ago by
ATpoint
76k • written 4 days ago by
vk
▴ 40
1
vote
4
replies
397
views
How to understand if a GWAS sample comes from Chromosome X or Y
python
26 days ago by
dzisis1986
▴ 60
308 results • Page
1 of 7
Recent Votes
Comment: Filtering VCF to divide with equal sizes
Answer: How to plot proportion of cells in each cluster with scanpy?
Comment: How the first sequencing product removed in pair end sequencing
Comment: WGCNA Labeled Heatmap
C: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
Comment: Hisat2 index and alignment question
A: Finding overlaps between GRanges objects
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Recent Replies
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I see the error message but I'm confused on what it's telling me.
Answer: Bacterial Pangenome Analysis
by
liorglic
★ 1.2k
I am not sure I understand why you think there is a problem with your analysis. It makes perfect sense that different blastp cutoffs produc…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you so much. That worked perfectly and it was much faster than what I was trying.
Answer: How to plot proportion of cells in each cluster with scanpy?
by
Radu Tanasa
▴ 60
Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level? ```py import pandas as p…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Why would that be an advantage?
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★ 1.2k
The following code will write percentage in your stacked barplot. cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
• 0
@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Because that was the code from the link. It is how they specified they had 2 groups of samples but I don't have 2 groups. Sorry for the con…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
bk11
★ 1.2k
No there is no bug in this. Please see carefully what the `error` message tells to you.
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
• 0
@michaeld Thanks. I tried it using STAR to map the transcript to the annotation gtf file, and was planning to use featureCounts/gene Counts…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bk11
★ 1.2k
Why you had `type` in your code above then?
Comment: Comparing multiple columns from two files using AWK
by
Ram
40k
R's dplyr will serve well here. ```r fileA %>% mutate(V3 = sub(V3, "chr","") %>% inner_join(fileB, join_by(V3 == chr, window_end <= V4, ..…
Comment: How to plot proportion of cells in each cluster with scanpy?
by
bioinfo
▴ 110
Thank you for the suggestion. Unfortunately, that does not work for me because I do not have a "type" argument in the adata.obs. I think th…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
seattlescientist_01
• 0
I'm still seeing errors: First I tried the code you mentioned except I use `clusters` instead of `embryo.time.bin` since this is a column…
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