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400 results • Page
5 of 8
Sort: Rank
Rank
Views
Votes
Replies
2
votes
9
replies
932
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 20 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
0
votes
11
replies
697
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
18 days ago by
atowns21
• 0
0
votes
1
reply
208
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 21 days ago by
bk11
★ 2.4k • written 21 days ago by
alphaflylizard
• 0
0
votes
0
replies
119
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
21 days ago by
ohtang7
▴ 40
0
votes
1
reply
202
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 21 days ago by
GenoMax
142k • written 21 days ago by
Srinka
▴ 20
0
votes
5
replies
417
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
20 days ago by
njornet
▴ 20
0
votes
0
replies
123
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 21 days ago by
Ram
43k • written 21 days ago by
SHREYA
• 0
0
votes
0
replies
126
views
Merging replicates from Encode project
CHIP-seq
encode
21 days ago by
Nurken
• 0
1
vote
3
replies
296
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
21 days ago by
WouterDeCoster
47k
1
vote
3
replies
331
views
some error in building kraken2 database
metagenome
kraken2
20 days ago by
Art1ess
• 0
0
votes
1
reply
205
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 21 days ago by
bk11
★ 2.4k • written 21 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
209
views
Failed kmer content
kmer
illumina
ngs
updated 21 days ago by
Ram
43k • written 21 days ago by
Kasturi
• 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 21 days ago by
Ram
43k • written 21 days ago by
SSSJec
• 0
0
votes
1
reply
173
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 22 days ago by
Ram
43k • written 22 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
449
views
Error in cnetplot enrichplot package
R
updated 22 days ago by
Ram
43k • written 22 days ago by
Farhad
• 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 22 days ago by
Ram
43k • written 22 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 22 days ago by
Ram
43k • written 22 days ago by
sansan_96
▴ 90
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 21 days ago by
Ram
43k • written 22 days ago by
Amélie
• 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 22 days ago by
Ram
43k • written 22 days ago by
Pine
▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 22 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
8
replies
527
views
Downsampling fastq file
downsample
fastq
14 days ago by
marco.barr
▴ 110
0
votes
1
reply
168
views
tbtool
tbtool
updated 22 days ago by
Ram
43k • written 22 days ago by
Raman
• 0
0
votes
10
replies
601
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 14 days ago by
i.sudbery
19k • written 22 days ago by
Patadu94
• 0
0
votes
1
reply
158
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 22 days ago by
ATpoint
82k • written 22 days ago by
enanoide
• 0
0
votes
0
replies
105
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
22 days ago by
manaswwm
▴ 510
0
votes
0
replies
96
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
21 days ago by
alifafiq1
• 0
0
votes
0
replies
101
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
22 days ago by
feather-W
• 0
2
votes
4
replies
370
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
20 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
98
views
Annotating single cell data automatically
cell
annotation
single
22 days ago by
Gerard
• 0
0
votes
1
reply
195
views
RNA-seq bacteria contamination
RNA-seq
updated 22 days ago by
GenoMax
142k • written 22 days ago by
sh
• 0
0
votes
0
replies
95
views
Imputation advice
imputation
22 days ago by
kl
▴ 10
0
votes
0
replies
115
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
22 days ago by
Enrique
• 0
0
votes
0
replies
91
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
22 days ago by
sativus
▴ 20
0
votes
0
replies
96
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
22 days ago by
Biostars2200
• 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 22 days ago by
Carlo Yague
8.7k • written 22 days ago by
Atul K.
• 0
2
votes
5
replies
528
views
Marking duplicates using UMIs
Deduplication
UMI
updated 22 days ago by
i.sudbery
19k • written 23 days ago by
Lipika
• 0
0
votes
0
replies
156
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 23 days ago by
Ram
43k • written 23 days ago by
sainavyav22
• 0
0
votes
0
replies
160
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
23 days ago by
rthapa
▴ 90
0
votes
0
replies
155
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
24 days ago by
Mamatha Y S
• 0
0
votes
2
replies
316
views
bam merging for archaic samples
samtools
bam
updated 23 days ago by
Ram
43k • written 24 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
560
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
24 days ago by
mathavanbioinfo
▴ 90
2
votes
5
replies
780
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 24 days ago by
Jesse
▴ 770 • written 25 days ago by
Ann
★ 2.4k
0
votes
0
replies
207
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 25 days ago by
Ram
43k • written 25 days ago by
mja
• 0
0
votes
0
replies
207
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
25 days ago by
Nitin
• 0
0
votes
0
replies
199
views
Chemical structure validation
structure
cap
validation
metabolite
25 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
300
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 25 days ago by
GenoMax
142k • written 25 days ago by
bioyas
▴ 10
0
votes
0
replies
231
views
Copy number variation plot
Copy-number-variation
genomics
updated 25 days ago by
Ram
43k • written 25 days ago by
Emmi
• 0
0
votes
0
replies
207
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
25 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
319
views
Could you please assist in identifying this cluster?
single-cell
updated 25 days ago by
Ram
43k • written 25 days ago by
carolofharvest
▴ 40
0
votes
0
replies
223
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 25 days ago by
Ram
43k • written 25 days ago by
Dinmukhamed
• 0
400 results • Page
5 of 8
Recent Votes
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
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Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Comment: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
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142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
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There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
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Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
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Thanks! Super helpful.
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4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
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142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
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does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
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Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
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