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675 results • Page
2 of 14
Sort: Views
Rank
Views
Votes
Replies
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 23 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
0
votes
6
replies
2.2k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 17 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
27 days ago by
anna
▴ 20
2
votes
6
replies
2.0k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 11 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
6
votes
6
replies
1.9k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 21 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 23 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 5 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
6
votes
5
replies
1.8k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
12 days ago by
Arton
▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 18 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 23 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 18 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 8 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 28 days ago by
Gordon Smyth
★ 7.2k • written 9 months ago by
Calum
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 13 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 18 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
22 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
3 days ago by
Aspire
▴ 330
1
vote
4
replies
1.2k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
24 days ago by
eebloom
▴ 80
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
22 days ago by
Ibrahim Tanyalcin
★ 1.2k
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 6 days ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
13
votes
14
replies
1.1k
views
High Malat-1 expression in single cell data
single-cell
updated 19 days ago by
t.montserrat.ayuso
▴ 40 • written 28 days ago by
carolofharvest
▴ 40
2
votes
11
replies
1.1k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 28 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
me
• 0
7
votes
16
replies
1.0k
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
28 days ago by
Ruqaiya
• 0
2
votes
5
replies
970
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 27 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
4
votes
11
replies
965
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
5 days ago by
J
▴ 10
1
vote
10
replies
925
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 21 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
3
replies
910
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 4 days ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
2
votes
3
replies
895
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 22 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
3
votes
8
replies
879
views
Random Access remote BAM files
htslib
BAM
updated 4 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
10
votes
14
replies
872
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 19 days ago by
GenoMax
142k • written 25 days ago by
nicole.kavanagh
• 0
7
votes
13
replies
844
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 3 days ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
1
vote
16
replies
835
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 8 days ago by
GenoMax
142k • written 11 days ago by
hophuquy0944
• 0
1
vote
5
replies
827
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
821
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 10 days ago by
sansan_96
▴ 90 • written 2.8 years ago by
boymin2020
▴ 80
0
votes
1
reply
813
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 24 days ago by
Ram
44k • written 2.7 years ago by
carov
• 0
2
votes
11
replies
811
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
10 days ago by
egascon
• 0
2
votes
9
replies
800
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 12 days ago by
Pierre Lindenbaum
162k • written 19 days ago by
schmince
• 0
0
votes
1
reply
795
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 28 days ago by
Francesco
▴ 10 • written 3.4 years ago by
gt
▴ 30
0
votes
3
replies
794
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 27 days ago by
weidonglu
• 0 • written 22 months ago by
JZX
• 0
1
vote
6
replies
787
views
anRichment is missing
WGCNA
anRichment
updated 20 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
0
votes
1
reply
769
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 21 days ago by
GenoMax
142k • written 22 days ago by
tulip
• 0
0
votes
2
replies
764
views
homer not configured properly
Homer
makeTagDirectory
updated 24 days ago by
clairechung112
• 0 • written 2.0 years ago by
amahdi779
• 0
3
votes
8
replies
762
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 20 days ago by
Chris Dean
▴ 410 • written 24 days ago by
sovrappensiero
▴ 100
1
vote
1
reply
741
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
2
votes
11
replies
740
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 19 hours ago by
Ram
44k • written 9 days ago by
hannes.bongartz
• 0
1
vote
2
replies
736
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 8 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
2
votes
4
replies
735
views
Count all variants from vcf file
variants
vcf
Count
updated 20 days ago by
Pierre Lindenbaum
162k • written 21 months ago by
t.ali
• 0
0
votes
1
reply
732
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 26 days ago by
Ram
44k • written 26 days ago by
Dr Huma Naz
• 0
5
votes
5
replies
717
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 23 days ago by
Mbofire
• 0 • written 4 weeks ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
715
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 18 days ago by
DGTool
▴ 20 • written 22 months ago by
yassine
• 0
675 results • Page
2 of 14
Recent Votes
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
Search within posts based on tags using the Biostars API
Extract ENSEMBL IDs from processed Seurat object instead of gene symbols
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Recent Replies
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
Varsha
• 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8?
by
Asaf
10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection
by
a.alnawfal.1992
▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score?
by
ATpoint
82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig
by
b.contreras.moreira
▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
Hello Pierre, Thanks for your reply and insight. with samtools view | grep using the erroneous CIGAR string I get: A00152:841:H7J22D…
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
please, show us the following output: samtools view "${Ind1}_sorted_dup.bam" | grep -F "A00152:841:H7J22DRX3:2:1112:5267:11397" Furth…
Comment: Failed to download data from EBI with ascp
by
孝中
• 0
Hi, have you found the solution to this problem?
Comment: samtools write-index
by
R.L.
• 0
Oh God, thank you so much for helping me in both platforms! I am gonna upgrade my samtools to stay tracked with you and your team! Thank yo…
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
jared.andrews07
★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR
by
jared.andrews07
★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
Couldn't tell you, I avoid Seurat like the plague.
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