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
50k
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
▴ 270
4
votes
4
replies
42k
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 6.2 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 8.4 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
29k
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 7.7 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 8.1 years ago by
GenoMax
142k • written 8.1 years ago by
31sharmajittu1991
• 0
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.8 years ago by
aggregatibacter
▴ 180
1
vote
5
replies
20k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 6.5 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 2.1 years ago by
Ram
43k • written 9.3 years ago by
lcc1844
▴ 40
2
votes
10
replies
18k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 2.7 years ago by
Ram
43k • written 8.6 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 2.1 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
5.9 years ago by
salamandra
▴ 550
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.8 years ago by
Shelle
▴ 30
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
1
vote
8
replies
17k
views
How to update rlang in R?
rlang
R
19 months ago by
Amr
▴ 160
1
vote
5
replies
17k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
6.1 years ago by
n85825
• 0
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
6.2 years ago by
demoraesdiogo2017
▴ 100
0
votes
3
replies
16k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 21 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 10.1 years ago by
Biostar
20 • written 10.6 years ago by
curious.genome
▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.4 years ago by
natasha.sernova
★ 4.0k • written 7.4 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 19 months ago by
Ram
43k • written 8.8 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
142k • written 6.0 years ago by
WUSCHEL
▴ 760
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
7.9 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 4.5 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
4
votes
1
reply
15k
views
Converting BigBed to Bed format
Installing BigFile Support
8.9 years ago by
sumaira.zaman10
▴ 20
1
vote
13
replies
15k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 3.0 years ago by
darklings
▴ 570 • written 4.6 years ago by
gordo2b
• 0
1
vote
8
replies
15k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
cafelumiere12
▴ 80
6
votes
13
replies
15k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
8.0 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
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
10.0 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 5.0 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 5.7 years ago by
Ram
43k • written 8.2 years ago by
Peng Huang
▴ 50
4
votes
12
replies
13k
views
STAR alignment error- Segmentation fault (core dumped)
alignment
software error
RNA-Seq
STAR
5.9 years ago by
EagleEye
7.5k
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
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
4.0 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 2.1 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 4.8 years ago by
Morris_Chair
▴ 360 • written 4.8 years ago by
limjustinj
• 0
0
votes
3
replies
13k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
7.1 years ago by
moxu
▴ 510
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
1,000 results • Page
1 of 20
Recent Votes
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
Answer: ggrepel function: geom_text_repel()
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Recent Locations •
All
Australia,
just now
India,
3 minutes ago
Chennai, India,
5 minutes ago
Bologna,
5 minutes ago
France,
5 minutes ago
Finland,
7 minutes ago
Belgium,
8 minutes ago
Recent Awards •
All
Teacher
to
Rob
6.6k
Popular Question
to
Nyksubuz
▴ 10
Popular Question
to
Govardhan Anande
▴ 150
Popular Question
to
Lhl
▴ 760
Popular Question
to
Takuma
▴ 20
Popular Question
to
BATMAN
• 0
Teacher
to
dario.garvan
▴ 520
Recent Replies
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Answer: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
by
Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range
by
Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Traffic: 1989 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