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686 results • Page
2 of 14
Sort: Views
Rank
Views
Votes
Replies
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
20 days ago by
anna
▴ 20
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 23 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 4 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 15 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 16 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
5 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 11 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 16 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 11 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 1 day 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 21 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 6 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 12 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 24 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
15 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
18 days ago by
eebloom
▴ 80
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
15 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 2 hours ago by
Ram
43k • written 5 months ago by
LauferVA
4.2k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
25 days ago by
DKA
▴ 40
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 21 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 0
2
votes
3
replies
1.0k
views
Method to detect genome doubling
CNV
genome doubling
updated 28 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
13
votes
14
replies
991
views
High Malat-1 expression in single cell data
single-cell
updated 12 days ago by
t.montserrat.ayuso
▴ 40 • written 21 days ago by
carolofharvest
▴ 40
7
votes
16
replies
982
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
21 days ago by
Ruqaiya
• 0
1
vote
8
replies
965
views
Adding CB tag to bam file
samtools
bam
updated 25 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Maria
• 0
2
votes
5
replies
961
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 21 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
9
replies
953
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 26 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
4
votes
11
replies
905
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 26 days ago by
LauferVA
4.2k • written 27 days ago by
dominickd
• 0
1
vote
10
replies
903
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 14 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
0
votes
2
replies
868
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 26 days ago by
barslmn
★ 2.2k • written 2.8 years ago by
jhy
▴ 10
2
votes
3
replies
858
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 16 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
10
votes
14
replies
827
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 13 days ago by
GenoMax
142k • written 19 days ago by
nicole.kavanagh
• 0
4
votes
6
replies
818
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 23 days ago by
dsull
★ 6.0k • written 27 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
810
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
1
reply
806
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 18 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
1
vote
3
replies
805
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 3 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
2
votes
5
replies
800
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 29 days ago by
Jesse
▴ 770 • written 4 weeks ago by
Ann
★ 2.4k
0
votes
1
reply
787
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 22 days ago by
Francesco
▴ 10 • written 3.4 years ago by
gt
▴ 30
0
votes
3
replies
778
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 20 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
4
votes
8
replies
775
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 23 days ago by
Alex Reynolds
35k • written 24 days ago by
J
▴ 10
8
votes
8
replies
773
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 25 days ago by
swbarnes2
14k • written 26 days ago by
Aaliya
▴ 10
3
votes
6
replies
769
views
Ciriquant not configuring hisat2 indexed files
ciriquant
28 days ago by
Atul K.
• 0
3
votes
4
replies
763
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
28 days ago by
rahu
• 0
3
votes
3
replies
760
views
KissDE and batch effect
kissDE
kissplice
28 days ago by
david.b.rombaut
▴ 10
1
vote
6
replies
757
views
anRichment is missing
WGCNA
anRichment
updated 13 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
1
vote
16
replies
756
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 2 days ago by
GenoMax
142k • written 5 days ago by
hophuquy0944
• 0
0
votes
2
replies
756
views
homer not configured properly
Homer
makeTagDirectory
updated 17 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
2
votes
9
replies
749
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 5 days ago by
Pierre Lindenbaum
161k • written 13 days ago by
schmince
• 0
2
votes
11
replies
738
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
3 days ago by
egascon
• 0
5
votes
4
replies
734
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
26 days ago by
kirillkirilenko
▴ 40
3
votes
8
replies
732
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 13 days ago by
Chris Dean
▴ 410 • written 17 days ago by
sovrappensiero
▴ 100
686 results • Page
2 of 14
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Answer: Generating Group/Cluster Lists from fastq files
The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
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C: Cleaning RNA-Seq data from rRNA
Answer: How to find identical sequences in genome fasta file (by Python or any possible
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Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
Answer: Error in using BioSampleParser tool: subscript out of bounds
by
Mohamed Samir
▴ 20
Dear marco, We need to ask ourselves why it is not working for all bioprojects ? I have looked into this, and observed that as long as the…
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43k
You ***want*** ~3000 DE genes?<a href="" title="Text added because biostars parser needs it"></a>
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by
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> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths
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beantkapoor16
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Hello, just wanted to check in if the code has been fixed yet? Thank you.
Comment: Super ehancers
by
jared.andrews07
★ 16k
Based on the [source code](https://bitbucket.org/young_computation/rose/src/feb35cb1d9556a76f8ac1f51521539bb30651343/ROSE_utils.py?at=maste…
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
Ram
43k
They're not addressing the actual question, just saying something tangentially related. It looks like their understanding of both consensus…
Comment: Super ehancers
by
Oburah
• 0
Hello, i encountered this problem when running ROSE, Do anyone know how to solve it? python2.7 ROSE_main.py -g HG38 -i /home/hesborn/…
Answer: How to generate an Upset plot in R to plot the shared variants between cell free
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Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array
by
fu_entomology
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We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
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I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
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Bioinformatics_begginner
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Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
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