Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
83 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
0
votes
11
replies
475
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
19 hours ago by
atowns21
• 0
2
votes
9
replies
822
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
8
replies
311
views
Error in cnetplot enrichplot package
R
updated 3 days ago by
Ram
43k • written 4 days ago by
Farhad
• 0
0
votes
7
replies
271
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
6
replies
427
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
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
0
votes
5
replies
291
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
2
votes
5
replies
685
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by
Jesse
▴ 740 • written 7 days ago by
Ann
★ 2.4k
0
votes
5
replies
293
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
2 days ago by
njornet
▴ 20
1
vote
5
replies
269
views
Downsampling fastq file
downsample
fastq
updated 4 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 80
2
votes
5
replies
451
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 5 days ago by
Lipika
• 0
2
votes
4
replies
266
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
2 days ago by
samuelkalandarov2002
▴ 10
0
votes
4
replies
250
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
3
replies
210
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
3
votes
3
replies
470
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
0
votes
2
replies
237
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 2 days ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
1
vote
2
replies
213
views
PCA plot
DESeq2
PCAplot
updated 10 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
1
vote
2
replies
233
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
0
votes
2
replies
170
views
Highest variable features in single cell data
single-cell
updated 23 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
221
views
Annovar using R package
Annovar
gnomAD
R
22 hours ago by
DKA
▴ 40
1
vote
2
replies
202
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
2
replies
261
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
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
132
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
414
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
0
votes
1
reply
131
views
tbtool
tbtool
updated 4 days ago by
Ram
43k • written 4 days ago by
Raman
• 0
0
votes
1
reply
150
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
1
reply
141
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
407
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
149
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
156
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
118
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
AaronJaime
• 0
0
votes
1
reply
146
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
benguyarenbeyaz98
• 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
143
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 3 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
0
votes
0
replies
80
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
22 hours ago by
simplitia
▴ 130
0
votes
0
replies
53
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
15 hours ago by
turcoa1
• 0
0
votes
0
replies
54
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
13 hours ago by
SineWave
• 0
1
vote
0
replies
55
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
12 hours ago by
KABILAN
▴ 50
0
votes
0
replies
77
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
10 hours ago by
HarperReed
• 0
0
votes
0
replies
37
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 3 hours ago by
Ram
43k • written 3 hours ago by
vanbelj
▴ 40
0
votes
0
replies
57
views
RNA-seq: full length gene
RNA-seq
updated 3 hours ago by
Ram
43k • written 13 hours ago by
Nargis
• 0
0
votes
0
replies
38
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 1 hour ago by
GenoMax
141k • written 4 hours ago by
hagl
▴ 10
0
votes
0
replies
18
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 10 minutes ago by
Ram
43k • written 1 hour ago by
Guille
• 0
0
votes
0
replies
259
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
2 days ago by
pramach1
▴ 40
0
votes
0
replies
212
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
5 days ago by
Mamatha Y S
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
5 days ago by
rthapa
▴ 90
83 results • Page
1 of 2
Recent Votes
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
Recent Locations •
All
Mexico,
just now
London, United Kingdom,
1 minute ago
United States,
2 minutes ago
Germany,
3 minutes ago
United States,
3 minutes ago
United States,
4 minutes ago
Gainesville, FL,
5 minutes ago
Recent Awards •
All
Popular Question
to
chaco001
▴ 40
Commentator
to
GenoMax
141k
Popular Question
to
rheab1230
▴ 140
Popular Question
to
BioinfGuru
★ 1.7k
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
Supporter
to
Jalil Sharif
▴ 80
Recent Replies
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…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 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
by
i.sudbery
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…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
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 :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Traffic: 2658 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6