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84 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
0
votes
11
replies
486
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
2
votes
9
replies
826
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 3 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
8
replies
319
views
Error in cnetplot enrichplot package
R
updated 4 days ago by
Ram
43k • written 4 days ago by
Farhad
• 0
0
votes
7
replies
303
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 11 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
6
replies
431
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 2 days ago by
gv
• 0 • written 25 days ago by
Srinka
▴ 20
0
votes
5
replies
296
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 1 day ago by
GenoMax
141k • written 2 days ago by
Bertalan_Takacs
▴ 90
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 6 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
2
votes
5
replies
686
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 6 days ago by
Jesse
▴ 740 • written 7 days ago by
Ann
★ 2.4k
1
vote
5
replies
272
views
Downsampling fastq file
downsample
fastq
updated 4 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 80
0
votes
5
replies
300
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
2 days ago by
njornet
▴ 20
2
votes
5
replies
452
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 6 days ago by
Lipika
• 0
2
votes
4
replies
269
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
2 days ago by
samuelkalandarov2002
▴ 10
0
votes
4
replies
254
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
1
vote
3
replies
216
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
1
vote
3
replies
254
views
some error in building kraken2 database
metagenome
kraken2
3 days ago by
Art1ess
• 0
0
votes
3
replies
214
views
Highest variable features in single cell data
single-cell
updated 6 hours ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
3
votes
3
replies
471
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 4 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
2
replies
227
views
Annovar using R package
Annovar
gnomAD
R
1 day ago by
DKA
▴ 40
1
vote
2
replies
235
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
1
vote
2
replies
204
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
2
replies
262
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
1
vote
2
replies
238
views
PCA plot
DESeq2
PCAplot
updated 18 hours ago by
ATpoint
82k • written 2 days ago by
Aaliya
▴ 10
0
votes
2
replies
239
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 2 days ago by
Ram
43k • written 3 days ago by
v.berriosfarias
▴ 140
0
votes
1
reply
149
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
143
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 2 days ago by
Sofia
• 0 • written 2 days ago by
mawigoj318
• 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 4 days ago by
Ram
43k • written 4 days ago by
Cameron.walker9900
• 0
0
votes
1
reply
418
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 1 day ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
1
reply
151
views
RNA-seq bacteria contamination
RNA-seq
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sh
• 0
0
votes
1
reply
157
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Srinka
▴ 20
0
votes
1
reply
129
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 1 day ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
1
vote
1
reply
167
views
Failed kmer content
kmer
illumina
ngs
updated 3 days ago by
Ram
43k • written 3 days ago by
Kasturi
• 0
0
votes
1
reply
126
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 4 days ago by
ATpoint
82k • written 4 days ago by
enanoide
• 0
0
votes
1
reply
137
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
417
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
0
votes
1
reply
132
views
tbtool
tbtool
updated 4 days ago by
Ram
43k • written 4 days ago by
Raman
• 0
0
votes
1
reply
156
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
alphaflylizard
• 0
0
votes
0
replies
92
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 day ago by
simplitia
▴ 130
0
votes
0
replies
67
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
23 hours ago by
turcoa1
• 0
1
vote
0
replies
69
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
20 hours ago by
KABILAN
▴ 50
0
votes
0
replies
97
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
18 hours ago by
HarperReed
• 0
0
votes
0
replies
57
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 10 hours ago by
Ram
43k • written 11 hours ago by
vanbelj
▴ 40
0
votes
0
replies
71
views
RNA-seq: full length gene
RNA-seq
updated 10 hours ago by
Ram
43k • written 21 hours ago by
Nargis
• 0
0
votes
0
replies
58
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 9 hours ago by
GenoMax
141k • written 12 hours ago by
hagl
▴ 10
0
votes
0
replies
71
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 hours ago by
Ram
43k • written 21 hours ago by
SineWave
• 0
0
votes
0
replies
75
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
5 hours ago by
biocellbio
• 0
1
vote
0
replies
542
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
6 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
31
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
3 hours ago by
O.rka
▴ 710
0
votes
0
replies
213
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
6 days ago by
abhishekghadge
• 0
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
6 days ago by
Mamatha Y S
• 0
84 results • Page
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Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Recent Replies
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
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★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
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19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
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If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
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