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 16 months ago by
Nicole
• 0 • written 5.9 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
34k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 21 months ago by
Qboy
▴ 10 • written 6.1 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
29k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 20 months ago by
Ram
43k • written 8.3 years ago by
dam4l
▴ 200
5
votes
6
replies
28k
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 7.7 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
21k
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 6.4 years ago by
ago1mutant
▴ 10
2
votes
8
replies
18k
views
Using vcfutils.pl command
alignment
updated 24 months 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
17k
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 24 months 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
18 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
5.0 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 9 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 3.8 years ago by
Ram
43k • written 3.8 years ago by
camillab.
▴ 160
1
vote
8
replies
15k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 24 months 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
8.8 years ago by
sumaira.zaman10
▴ 20
4
votes
1
reply
15k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
7.2 years ago by
ZheFrench
▴ 570
6
votes
13
replies
15k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
7.9 years ago by
rob.costa1234
▴ 310
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
7.1 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
4.1 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 7.2 years ago by
Medhat
9.7k • written 7.2 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 9.2 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 18 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 7.4 years ago by
Biostar
20 • written 7.6 years ago by
zh.khodadadi
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: Sheep reference genome remapping coordinates
Answer: Sheep reference genome remapping coordinates
DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
Recent Locations •
All
Stony Brook University, NY,
1 minute ago
Spain,
2 minutes ago
United Kingdom,
3 minutes ago
Italy,
4 minutes ago
Netherlands,
4 minutes ago
United Kingdom,
5 minutes ago
Berlin,
6 minutes ago
Recent Awards •
All
Scholar
to
Juke34
8.5k
Scholar
to
GenoMax
141k
Popular Question
to
carlopecoraro2
★ 2.5k
Student
to
manaswiniparija3
▴ 40
Popular Question
to
tomas4482
▴ 390
Popular Question
to
vinayjrao
▴ 250
Scholar
to
Scooter
▴ 280
Recent Replies
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies
by
GenoMax
141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
by
GenoMax
141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
GenoMax
141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq
by
GenoMax
141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Jacky
• 0
I got it, thank you for your response.
Answer: DEseq2
by
ATpoint
81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference?
by
Ehsan
• 0
Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version
by
manaswwm
▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Juke34
8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
Dave Carlson
★ 1.7k
You're allocating 4 compute nodes (`#SBATCH -N 4`), but STAR can't actually make use of more than 1 compute node. You can increase the num…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Dave Carlson
★ 1.7k
```conda install -y bioconda::packageX conda-forge::packageY``` should do what you're looking for.
Comment: Supergnova stuck in tutorial
by
Murat
• 0
Hi GenoMax, Thank you for your advice. I sent an email to them and have already opened an issue on Github. Let see if there is any other so…
Traffic: 2673 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