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Limit : this week
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87 results • Page
1 of 2
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0
votes
1
reply
11
views
Multiplexing for pooled CRISPR screen sequencing
Illumina
multiplex
CRISPR-screen
updated just now by
Ram
44k • written 27 minutes ago by
Tuấn Anh
• 0
0
votes
0
replies
12
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated just now by
Ram
44k • written 44 minutes ago by
Arton
▴ 10
0
votes
2
replies
82
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
2 hours ago by
Shukai
• 0
0
votes
0
replies
37
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
LuciaNhu
• 0
1
vote
2
replies
77
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 1 hour ago by
Ram
44k • written 4 hours ago by
Harshita
• 0
2
votes
0
replies
44
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
Bioinformatics
csaw
4 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
45
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
Christopher
• 0
0
votes
1
reply
72
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 4 hours ago by
DBScan
▴ 300 • written 5 hours ago by
brunomiwa
• 0
0
votes
0
replies
44
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
6 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
102
views
Generating a Bed file from a Fasta file
bedfile
Sequences
Random
NullSeq
updated 5 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
pirku
• 0
0
votes
0
replies
52
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
9 hours ago by
Yao
▴ 30
0
votes
0
replies
58
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
11 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
148
views
Where to find old version of GATK best practice
gatk
2 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
84
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 11 hours ago by
Pierre Lindenbaum
161k • written 12 hours ago by
Peter Chung
▴ 200
0
votes
1
reply
96
views
CreateSeuratObject taking very long
seurat
updated 6 hours ago by
Nitin Narwade
★ 1.6k • written 16 hours ago by
eae6d2e7
• 0
0
votes
0
replies
65
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
17 hours ago by
Christopher
• 0
0
votes
2
replies
159
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
5 hours ago by
Bjorn
• 0
0
votes
3
replies
218
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 22 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
0
votes
1
reply
112
views
vcf phasing
beagle
WhatsHap
phasing
updated 7 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
0
votes
0
replies
83
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
ev97
▴ 20
0
votes
1
reply
130
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 1 day ago by
marco.barr
▴ 130 • written 1 day ago by
sooni
▴ 20
0
votes
1
reply
98
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jinyi
• 0
0
votes
0
replies
75
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
1 day ago by
V_Vibes
• 0
0
votes
0
replies
144
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 23 hours ago by
Ram
44k • written 1 day ago by
JorgeVallejo
▴ 20
0
votes
0
replies
96
views
transcriptome annotation
annotation
trinity
transcriptome
updated 1 day ago by
Ram
44k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
222
views
Why most genes have high padj values
RNA-seq
DEG
updated 1 day ago by
Ram
44k • written 1 day ago by
mnx0723
• 0
0
votes
1
reply
141
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 1 day ago by
zx8754
11k • written 1 day ago by
Ali
• 0
0
votes
4
replies
244
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
100
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
1 day ago by
Maryam
• 0
1
vote
8
replies
445
views
Add stats to the plot
R
updated 11 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
0
votes
4
replies
329
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
0
votes
0
replies
111
views
handling bio replicates for chromHMM
replicates
chromHMM
2 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
102
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
2 days ago by
DGTool
▴ 20
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 23 hours ago by
Ram
44k • written 2 days ago by
Rodolfo Adrián
• 0
1
vote
2
replies
353
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 26 minutes ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
136
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
144
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
3 days ago by
Moinuddin
• 0
0
votes
1
reply
187
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Jacek
▴ 20
0
votes
0
replies
145
views
How can i use ESM-1v ?
VEP
ESM-1v
3 days ago by
Meto
• 0
0
votes
0
replies
157
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Long
• 0
0
votes
0
replies
149
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
4 days ago by
kilcdincer
▴ 10
0
votes
0
replies
163
views
genomic region of transcription factor
search
HOMER
motif
4 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
380
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 4 days ago by
dthorbur
★ 2.0k • written 4 days ago by
BATMAN
• 0
0
votes
6
replies
372
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
3 days ago by
hannes.bongartz
• 0
0
votes
0
replies
150
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 4 days ago by
GenoMax
142k • written 4 days ago by
yura.grabovska
▴ 90
1
vote
1
reply
206
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
1
vote
6
replies
355
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
7 hours ago by
Umer
▴ 50
0
votes
2
replies
258
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
melissachua90
▴ 70
0
votes
0
replies
137
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
4 days ago by
Varsha
• 0
0
votes
1
reply
450
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 4 days ago by
GenoMax
142k • written 4 days ago by
huxiangyulove
• 0
87 results • Page
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Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
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Comment: Super ehancers
by
jared.andrews07
★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
finch
• 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
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