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 : all time
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
22
replies
49k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 17 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 260
4
votes
4
replies
41k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 7.6 years ago by
entheologist33
▴ 100
4
votes
13
replies
35k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 22 months ago by
Qboy
▴ 10 • written 6.1 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.3 years ago by
dam4l
▴ 200
5
votes
6
replies
29k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools
linux
data
5.0 years ago by
star
▴ 350
2
votes
3
replies
28k
views
How to extract vcf.gz and vcf.gz.tbi
SNP
sequence
gene
updated 5.8 years ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
elhlalisoufiane
▴ 30
3
votes
4
replies
23k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 7.6 years ago by
Biostar
20 • written 7.8 years ago by
cookm346
▴ 20
13
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
7.0 years ago by
ariel.balter
▴ 260
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.4 years ago by
Leite
★ 1.3k
3
votes
3
replies
21k
views
Subsetting - Raw Counts from Seurat Object
seurat
raw counts
RNA-Seq
4.0 years ago by
David_emir
▴ 490
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R
MicroRNA TXT FORMAT
updated 8.0 years ago by
GenoMax
141k • written 8.0 years ago by
31sharmajittu1991
• 0
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.7 years ago by
aggregatibacter
▴ 180
1
vote
5
replies
19k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 6.4 years ago by
eteleeb
• 0 • written 6.5 years ago by
ago1mutant
▴ 10
2
votes
8
replies
18k
views
Using vcfutils.pl command
alignment
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
lcc1844
▴ 40
2
votes
10
replies
18k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 2.6 years ago by
Ram
43k • written 8.5 years ago by
cyril-cros
▴ 950
13
votes
13
replies
18k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.7 years ago by
Arindam Ghosh
▴ 510
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.8 years ago by
salamandra
▴ 550
2
votes
13
replies
17k
views
convert text file to fasta file
blast
updated 7.7 years ago by
GouthamAtla
12k • written 7.7 years ago by
sukesh1411
▴ 30
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.7 years ago by
Shelle
▴ 30
1
vote
8
replies
17k
views
How to update rlang in R?
rlang
R
19 months ago by
Amr
▴ 160
1
vote
5
replies
16k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
6.0 years ago by
n85825
• 0
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
6.1 years ago by
demoraesdiogo2017
▴ 100
0
votes
3
replies
16k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 20 months ago by
Ram
43k • written 8.5 years ago by
amyfm
▴ 10
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 10.0 years ago by
Biostar
20 • written 10.5 years ago by
curious.genome
▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.3 years ago by
natasha.sernova
★ 4.0k • written 7.3 years ago by
elisheva
▴ 120
3
votes
8
replies
16k
views
Error when running pheatmap
pheatmap
Error in hclust
5.1 years ago by
luzglongoria
▴ 50
2
votes
4
replies
16k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 18 months ago by
Ram
43k • written 8.7 years ago by
meekadi
▴ 10
4
votes
10
replies
16k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 6.0 years ago by
GenoMax
141k • written 6.0 years ago by
WUSCHEL
▴ 750
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
7.8 years ago by
Ric
▴ 430
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Shahzad
▴ 30
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 4.4 years ago by
schroder.julia
• 0 • written 6.8 years ago by
Jokhe
▴ 140
0
votes
3
replies
15k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap
R
RNA-Seq
annotations
updated 3.9 years ago by
Ram
43k • written 3.9 years ago by
camillab.
▴ 160
1
vote
8
replies
15k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
cafelumiere12
▴ 80
4
votes
1
reply
15k
views
Converting BigBed to Bed format
Installing BigFile Support
8.9 years ago by
sumaira.zaman10
▴ 20
6
votes
13
replies
15k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
7.9 years ago by
rob.costa1234
▴ 310
4
votes
1
reply
15k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
7.3 years ago by
ZheFrench
▴ 570
1
vote
13
replies
15k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.9 years ago by
darklings
▴ 570 • written 4.5 years ago by
gordo2b
• 0
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.2 years ago by
Patrick Brennan
▴ 50
0
votes
3
replies
14k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
9.9 years ago by
ira_grich
• 0
0
votes
2
replies
14k
views
Error in -delete: invalid argument to unary operator
RNA-Seq
R
4.2 years ago by
ovariohisterectomia
▴ 40
6
votes
13
replies
14k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 4.9 years ago by
zx8754
11k • written 6.4 years ago by
Farbod
★ 3.4k
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
Peng Huang
▴ 50
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 7.3 years ago by
Medhat
9.7k • written 7.3 years ago by
Sanchita Gupta
▴ 30
4
votes
12
replies
13k
views
STAR alignment error- Segmentation fault (core dumped)
alignment
software error
RNA-Seq
STAR
5.8 years ago by
EagleEye
7.5k
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
3.9 years ago by
Thorerges
▴ 10
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 2.0 years ago by
Ram
43k • written 9.3 years ago by
noushin.farnoud
▴ 130
0
votes
2
replies
13k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq
GSEA
gene
genome
updated 4.7 years ago by
Morris_Chair
▴ 350 • written 4.7 years ago by
limjustinj
• 0
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Debbie
▴ 10
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.5 years ago by
Biostar
20 • written 7.7 years ago by
zh.khodadadi
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Comment: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Recent Locations •
All
France/Nantes/Institut du Thorax - INSERM UMR1087,
just now
Mt. Pleasant, MI,
just now
United States,
2 minutes ago
United States,
5 minutes ago
United States,
5 minutes ago
Nigeria,
5 minutes ago
Palau,
10 minutes ago
Recent Awards •
All
Scholar
to
Alex Reynolds
35k
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
Recent Replies
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
★ 2.4k
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…
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…
Traffic: 2230 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