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117,012 results • Page
1 of 2341
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0
votes
0
replies
18
views
handling bio replicates for chromHMM
replicates
chromHMM
1 hour ago by
Hasan_Daaboul
• 0
0
votes
0
replies
15
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
1 hour ago by
DGTool
▴ 20
0
votes
1
reply
58
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
rj.rezwan
• 0
0
votes
2
replies
232
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
4 hours ago by
Ezequiel
• 0
0
votes
1
reply
71
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
updated 2 hours ago by
ATpoint
82k • written 7 hours ago by
Bibi
• 0
0
votes
1
reply
87
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 7 hours ago by
ATpoint
82k • written 13 hours ago by
KHURRAM SHAHZAD
• 0
798
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
1
reply
88
views
Add stats to the plot
R
stats
plotting
updated 6 hours ago by
GenoMax
142k • written 9 hours ago by
Ghada
• 0
1
vote
0
replies
67
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
9 hours ago by
micah
▴ 10
0
votes
0
replies
62
views
problems in installing rDock
rDock
make
Installation
Error
12 hours ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 13 hours ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
662
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 14 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
1
reply
283
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 20 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
0
votes
0
replies
87
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Mohamed Samir
▴ 20
0
votes
0
replies
93
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
1 day ago by
Moinuddin
• 0
0
votes
1
reply
132
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Jacek
▴ 20
2
votes
1
reply
199
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 19 hours ago by
Gordon Smyth
★ 7.2k • written 1 day ago by
marineandriot
• 0
0
votes
0
replies
103
views
How can i use ESM-1v ?
VEP
ESM-1v
1 day ago by
Meto
• 0
0
votes
0
replies
109
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Long
• 0
0
votes
2
replies
211
views
Trimming tool
Trimmer
tool
updated 1 day ago by
ntsopoul
▴ 60 • written 2 days ago by
GeneC
• 0
0
votes
0
replies
106
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
2 days ago by
kilcdincer
▴ 10
0
votes
2
replies
214
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
ijarne
• 0
0
votes
0
replies
130
views
genomic region of transcription factor
search
HOMER
motif
2 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
338
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 2 days ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
0
votes
6
replies
323
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
0
votes
0
replies
112
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 2 days ago by
GenoMax
142k • written 2 days ago by
yura.grabovska
▴ 90
4
votes
7
replies
504
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 2 days ago by
marco.barr
▴ 130 • written 4 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
169
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
0
votes
2
replies
186
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
3 hours ago by
Umer
▴ 50
0
votes
4
replies
320
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 1 day ago by
txema.heredia
▴ 130 • written 2 days ago by
Ngrin
• 0
4
votes
9
replies
466
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
2 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
225
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
0
votes
0
replies
113
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
2 days ago by
Varsha
• 0
0
votes
1
reply
348
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 2 days ago by
GenoMax
142k • written 2 days ago by
huxiangyulove
• 0
0
votes
0
replies
132
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
2 days ago by
O.rka
▴ 720
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 2 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
317
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
142
views
Use of ichor CNA
Dog
CNA
genome
3 days ago by
sainavyav22
• 0
2
votes
2
replies
258
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
txema.heredia
▴ 130
1
vote
0
replies
151
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 2 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
336
views
Details on salmon index
Salmon
updated 2 days ago by
Rob
6.6k • written 3 days ago by
Lorenzo
• 0
0
votes
0
replies
144
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
3 days ago by
Jsarria.EEAD
• 0
0
votes
1
reply
198
views
How can I calculate the OS of each patient?
overall-survival
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Pedro
• 0
1
vote
1
reply
206
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 3 days ago by
Ram
43k • written 3 days ago by
m90
▴ 30
0
votes
0
replies
141
views
cat-bgen fail
bgenix
updated 3 days ago by
Ram
43k • written 3 days ago by
lambard
• 0
3
votes
4
replies
324
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 2 days ago by
Jeremy Leipzig
22k • written 3 days ago by
Ali
• 0
3
votes
3
replies
244
views
getting exon coordinates
genomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Xbox_27
• 0
0
votes
4
replies
322
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 2 days ago by
Tony
• 0 • written 3 days ago by
vk
▴ 10
1
vote
5
replies
312
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 2 days ago by
Ram
43k • written 3 days ago by
manuelmourato25
• 0
3
votes
4
replies
406
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Pierre Lindenbaum
161k
117,012 results • Page
1 of 2341
Recent Votes
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
Answer: Duplicated sequence samtools
Answer: How to add Ensembl id to cluster.markers in Seurat
Sequence alignment on split read event such as inversion, duplication and complex nested events.
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
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scideas
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Recent Replies
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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