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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
2
replies
224
views
singlecell annotation
scRNA-seq
annotation
1 day ago by
kayah
• 0
0
votes
1
reply
145
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 2 days ago by
zx8754
11k • written 2 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
0
replies
105
views
t2t Reference gtf file
t2t
2 days ago by
Emre
• 0
1
vote
2
replies
228
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
0
votes
0
replies
106
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
2 days ago by
Yingying
• 0
0
votes
0
replies
104
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
PBC
▴ 10
0
votes
4
replies
248
views
Parsing fasta file by coordinates
linux
fasta
updated 1 hour ago by
Joe
21k • written 2 days ago by
sorrymouse
▴ 120
0
votes
2
replies
215
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
1 day ago by
eesiribloom
▴ 50
0
votes
0
replies
87
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
2 days ago by
erbrocato
• 0
0
votes
1
reply
127
views
Can I have multiple active GDC download tokens?
TCGA
updated 2 days ago by
GenoMax
140k • written 2 days ago by
mrk
• 0
0
votes
0
replies
103
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
barrypraveen
▴ 130
1
vote
2
replies
222
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
MAPK2
▴ 40
0
votes
0
replies
83
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 2 days ago by
Ram
43k • written 2 days ago by
La52dA97b6
• 0
0
votes
2
replies
198
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 2 days ago by
Ram
43k • written 2 days ago by
Bioinfonext
▴ 460
1
vote
0
replies
96
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
2 days ago by
mrazib0210
▴ 10
0
votes
1
reply
145
views
NCBI gene data
Variants
NCBI
updated 2 days ago by
GenoMax
140k • written 2 days ago by
chandrakala.m
• 0
0
votes
1
reply
139
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 2 days ago by
Ram
43k • written 2 days ago by
Sony
▴ 10
1
vote
0
replies
108
views
checkm lineage.ms output file
checkm
lineage
3 days ago by
A_heath
▴ 160
0
votes
0
replies
95
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 2 days ago by
Ram
43k • written 3 days ago by
Biogeek
• 0
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
0
votes
0
replies
83
views
Public datasets for genome-wide level mRNA-protein correlation calculation?
mRNA
protein
correlation
3 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 3 days ago by
Carlo Yague
8.6k • written 3 days ago by
anne
• 0
0
votes
1
reply
155
views
Difference in relative abundance between MicrobiomeDB and r phyloseq
phyloseq
updated 3 days ago by
Chris Dean
▴ 390 • written 3 days ago by
benkosta
• 0
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
4 days ago by
rheab1230
▴ 140
0
votes
0
replies
146
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
5 days ago by
asmariyaz23
▴ 10
0
votes
1
reply
200
views
Getting error in alignment using STAR
STAR
Error
updated 5 days ago by
Michael
54k • written 5 days ago by
pavithra.bioinformatics
• 0
0
votes
1
reply
225
views
PCA script correction
correction
script
PCA
updated 5 days ago by
BioinfGuru
★ 1.6k • written 5 days ago by
prity6459
• 0
1
vote
13
replies
963
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 2 days ago by
lcj34
▴ 410 • written 8 days ago by
b.contreras.moreira
▴ 70
0
votes
2
replies
286
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
0
votes
0
replies
177
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
5 days ago by
enee
▴ 10
0
votes
9
replies
426
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 1 hour ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
0
replies
163
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
6 days ago by
mb
• 0
0
votes
0
replies
164
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
6 days ago by
Apex92
▴ 280
0
votes
3
replies
297
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
5 days ago by
kabir.deb
▴ 80
0
votes
0
replies
178
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
6 days ago by
Minh
• 0
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
6 days ago by
applepie
• 0
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
0
replies
177
views
Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"
SCTransform
updated 6 days ago by
Ram
43k • written 6 days ago by
Anisha
• 0
0
votes
0
replies
170
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
6 days ago by
sakura
• 0
0
votes
0
replies
173
views
Example - Meta Analysis TCGA and DepMap
Meta-Analysis
TCGA
DepMap
updated 6 days ago by
Ram
43k • written 6 days ago by
joseph.landry
▴ 50
0
votes
1
reply
198
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Smilesky
• 0
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
5 days ago by
tujuchuanli
▴ 100
2
votes
1
reply
207
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 6 days ago by
Ram
43k • written 7 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
135
views
Tool for power calculation in GWAS for quantative trait
trait
quantative
power
calculation
GWAS
7 days ago by
chevivien
▴ 90
1
vote
1
reply
278
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 7 days ago by
dthorbur
★ 1.7k • written 7 days ago by
ekirsch
• 0
1
vote
3
replies
251
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Sony
▴ 10
0
votes
1
reply
185
views
PEAR seems to have sense to me
PEAR
updated 7 days ago by
GenoMax
140k • written 7 days ago by
ManuelDB
▴ 80
0
votes
1
reply
170
views
Interprete plot of dispersion estimation by DESeq2
dispersion
DEXseq
DESeq2
updated 7 days ago by
Pierre Lindenbaum
160k • written 7 days ago by
tien
▴ 10
1,000 results • Page
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A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
Crispr-cas9 screen analysis mageck
Comment: Issue with making local BLAST database
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
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▴ 20
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160k
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Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Comment: Issue with making local BLAST database
by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
Comment: Flow Cytometry Data Analysis by Seurat
by
ATpoint
81k
> I think Seurat is suitable for our purpose (e.g. conducting dimensional reduction of the data such as tSNE), but does it make sense? No…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
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