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683 results • Page
2 of 14
Sort: Views
Rank
Views
Votes
Replies
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 18 days ago by
i.sudbery
19k • written 21 days ago by
noodle
▴ 580
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 15 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 9 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
19 days ago by
anna
▴ 20
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 22 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 28 days ago by
ATpoint
82k • written 29 days ago by
BioinfGuru
★ 1.7k
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 3 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 13 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 15 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
4 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 10 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 15 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 10 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 20 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 28 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 40 minutes ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 860
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 5 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 10 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 22 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
13 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
16 days ago by
eebloom
▴ 80
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
13 days ago by
Ibrahim Tanyalcin
★ 1.2k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
24 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 19 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 0
2
votes
3
replies
998
views
Method to detect genome doubling
CNV
genome doubling
updated 26 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
1
vote
8
replies
958
views
Adding CB tag to bam file
samtools
bam
updated 23 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Maria
• 0
2
votes
5
replies
958
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 19 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
13
votes
14
replies
958
views
High Malat-1 expression in single cell data
single-cell
updated 11 days ago by
t.montserrat.ayuso
▴ 40 • written 19 days ago by
carolofharvest
▴ 40
7
votes
16
replies
958
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
19 days ago by
Ruqaiya
• 0
2
votes
9
replies
944
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 25 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
1
vote
10
replies
896
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 13 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
4
votes
11
replies
896
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 25 days ago by
LauferVA
4.2k • written 26 days ago by
dominickd
• 0
0
votes
2
replies
867
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 24 days ago by
barslmn
★ 2.2k • written 2.8 years ago by
jhy
▴ 10
2
votes
3
replies
853
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 14 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
1
vote
5
replies
815
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 29 days ago by
BioinfGuru
★ 1.7k • written 4 weeks ago by
rrehimi
• 0
4
votes
6
replies
811
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 22 days ago by
dsull
★ 6.0k • written 26 days ago by
qudrat.nii
▴ 10
0
votes
1
reply
806
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 16 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
1
vote
3
replies
801
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 2 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
10
votes
14
replies
797
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 11 days ago by
GenoMax
142k • written 17 days ago by
nicole.kavanagh
• 0
2
votes
5
replies
791
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 28 days ago by
Jesse
▴ 770 • written 29 days 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 20 days ago by
Francesco
▴ 10 • written 3.4 years ago by
gt
▴ 30
4
votes
8
replies
773
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 22 days ago by
Alex Reynolds
35k • written 23 days ago by
J
▴ 10
0
votes
3
replies
772
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 19 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
8
votes
8
replies
767
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 24 days ago by
swbarnes2
14k • written 25 days ago by
Aaliya
▴ 10
3
votes
6
replies
761
views
Ciriquant not configuring hisat2 indexed files
ciriquant
27 days ago by
Atul K.
• 0
5
votes
3
replies
760
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 29 days ago by
Enrique
• 0 • written 10 months ago by
Denis
▴ 310
3
votes
4
replies
756
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
26 days ago by
rahu
• 0
3
votes
3
replies
755
views
KissDE and batch effect
kissDE
kissplice
26 days ago by
david.b.rombaut
▴ 10
0
votes
2
replies
754
views
homer not configured properly
Homer
makeTagDirectory
updated 16 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
683 results • Page
2 of 14
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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scideas
▴ 30
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Muhammad
• 0
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synat.keam
▴ 100
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★ 1.8k
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Recent Replies
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…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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