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
45k
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 12 months ago by
Nicole
• 0 • written 5.6 years ago by
gaelgarcia
▴ 250
4
votes
4
replies
38k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 7.2 years ago by
entheologist33
▴ 100
4
votes
13
replies
32k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 17 months ago by
Qboy
• 0 • written 5.8 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
28k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 16 months ago by
Ram
41k • written 7.9 years ago by
dam4l
▴ 200
2
votes
3
replies
27k
views
How to extract vcf.gz and vcf.gz.tbi
SNP
sequence
gene
updated 5.4 years ago by
Pierre Lindenbaum
158k • written 5.4 years ago by
elhlalisoufiane
▴ 30
5
votes
6
replies
27k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools
linux
data
4.6 years ago by
star
▴ 350
3
votes
4
replies
22k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
cookm346
▴ 20
9
votes
4
replies
22k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
6.6 years ago by
ariel.balter
▴ 220
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R
MicroRNA TXT FORMAT
updated 7.7 years ago by
GenoMax
136k • written 7.7 years ago by
31sharmajittu1991
• 0
27
votes
17
replies
20k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.0 years ago by
Leite
★ 1.3k
7
votes
16
replies
19k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.4 years ago by
aggregatibacter
▴ 180
3
votes
3
replies
19k
views
Subsetting - Raw Counts from Seurat Object
seurat
raw counts
RNA-Seq
3.6 years ago by
David_emir
▴ 470
1
vote
5
replies
19k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 6.0 years ago by
eteleeb
• 0 • written 6.1 years ago by
ago1mutant
▴ 10
2
votes
8
replies
17k
views
Using vcfutils.pl command
alignment
updated 19 months ago by
Ram
41k • written 8.8 years ago by
lcc1844
▴ 40
2
votes
10
replies
17k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 2.3 years ago by
Ram
41k • written 8.2 years ago by
cyril-cros
▴ 950
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 19 months ago by
Ram
41k • written 8.8 years ago by
Mo
▴ 920
2
votes
13
replies
16k
views
convert text file to fasta file
blast
updated 7.3 years ago by
GouthamAtla
12k • written 7.3 years ago by
sukesh1411
▴ 30
16
votes
14
replies
16k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.5 years ago by
salamandra
▴ 550
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 9.6 years ago by
Biostar
20 • written 10.1 years ago by
curious.genome
▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.0 years ago by
natasha.sernova
★ 3.9k • written 7.0 years ago by
elisheva
▴ 120
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
5.8 years ago by
demoraesdiogo2017
▴ 100
13
votes
13
replies
16k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.3 years ago by
Arindam Ghosh
▴ 510
0
votes
3
replies
15k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 15 months ago by
Ram
41k • written 8.1 years ago by
amyfm
▴ 10
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
7.4 years ago by
Ric
▴ 430
4
votes
10
replies
15k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 5.6 years ago by
GenoMax
136k • written 5.6 years ago by
WUSCHEL
▴ 720
1
vote
5
replies
15k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
5.7 years ago by
n85825
• 0
2
votes
4
replies
15k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 13 months ago by
Ram
41k • written 8.4 years ago by
meekadi
▴ 10
4
votes
18
replies
15k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.1 years ago by
Biostar
20 • written 5.3 years ago by
Shelle
▴ 30
1
vote
8
replies
15k
views
How to update rlang in R?
rlang
R
14 months ago by
Amr
▴ 140
3
votes
8
replies
15k
views
Error when running pheatmap
pheatmap
Error in hclust
4.7 years ago by
luzglongoria
▴ 50
8
votes
4
replies
14k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 4.1 years ago by
schroder.julia
• 0 • written 6.4 years ago by
Jokhe
▴ 140
1
vote
8
replies
14k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 19 months ago by
Ram
41k • written 8.8 years ago by
cafelumiere12
▴ 80
3
votes
1
reply
14k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
6.9 years ago by
ZheFrench
▴ 540
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
9.5 years ago by
ira_grich
• 0
9
votes
13
replies
14k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 5 months ago by
Ram
41k • written 5.2 years ago by
Shahzad
▴ 30
9
votes
13
replies
14k
views
GC Content of Fasta file --- Python Help
sequence
6.8 years ago by
Patrick Brennan
▴ 50
6
votes
13
replies
14k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
7.5 years ago by
rob.costa1234
▴ 310
4
votes
1
reply
14k
views
Converting BigBed to Bed format
Installing BigFile Support
8.5 years ago by
sumaira.zaman10
▴ 20
0
votes
3
replies
14k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap
R
RNA-Seq
annotations
updated 3.5 years ago by
Ram
41k • written 3.5 years ago by
camillab.
▴ 160
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq
R
3.8 years ago by
ovariohisterectomia
▴ 40
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 5.3 years ago by
Ram
41k • written 7.8 years ago by
Peng Huang
▴ 50
6
votes
13
replies
13k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 4.5 years ago by
zx8754
11k • written 6.0 years ago by
Farbod
★ 3.4k
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 6.9 years ago by
Medhat
9.7k • written 6.9 years ago by
Sanchita Gupta
▴ 30
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 20 months ago by
Ram
41k • written 8.9 years ago by
noushin.farnoud
▴ 120
1
vote
13
replies
13k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.5 years ago by
darklings
▴ 560 • written 4.2 years ago by
gordo2b
• 0
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 14 months ago by
Ram
41k • written 8.3 years ago by
Debbie
▴ 10
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
3.6 years ago by
Thorerges
▴ 10
4
votes
12
replies
13k
views
STAR alignment error- Segmentation fault (core dumped)
alignment
software error
RNA-Seq
STAR
5.4 years ago by
EagleEye
7.5k
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.1 years ago by
Biostar
20 • written 7.3 years ago by
zh.khodadadi
▴ 20
0
votes
2
replies
12k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq
GSEA
gene
genome
updated 4.4 years ago by
Morris_Chair
▴ 340 • written 4.4 years ago by
limjustinj
• 0
1,000 results • Page
1 of 20
Recent Votes
Answer: Can't install hisat2 with miniconda
Answer: Can't install hisat2 with miniconda
Answer: iqtree vs raxml
Comment: which statistical test and which package for comapre datasets?
Answer: Bowtie 2 alignment
Answer: GO, KEGG, GSEA analysis with ~5 DEGs
Comment: GATK GetPileupSummaries Java heap space
Recent Locations •
All
United States,
4 minutes ago
Macao,
7 minutes ago
United States,
10 minutes ago
State College, PA, Penn State,
21 minutes ago
Russia,
29 minutes ago
United States,
30 minutes ago
United States,
37 minutes ago
Recent Awards •
All
Popular Question
to
jaredbernard
▴ 20
Popular Question
to
Tanvir Ahamed
▴ 350
Popular Question
to
Mr Locuace
▴ 150
Popular Question
to
Jeremy Leipzig
22k
Popular Question
to
satva72
• 0
Scholar
to
Istvan Albert
99k
Teacher
to
Rob
6.3k
Recent Replies
Comment: Can't install hisat2 with miniconda
by
Ozymandeus
▴ 30
Thank you! This fixed the issue.
Comment: Tutorials for Spatial Transcriptomics
by
CTLong
▴ 50
Although I'm not that into ST, but personally, when I learn a new technology, I usually play around with the data that had already been gen…
Comment: Is interleaved Fastq files the same as interlaced fastq
by
GenoMax
136k
> SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq Both programs will accept separate paired-end files. The reads in the …
Comment: which statistical test and which package for comapre datasets?
by
LauferVA
3.8k
@414fa591 this question is in need of clarification, as @rpolicastro has already said. However, based on what you've written, ***the resea…
Comment: Bowtie 2 alignment
by
Elizabeth
▴ 30
Thank you so much. I'm getting comparable results now. Appreciate the quick response.
Comment: which statistical test and which package for comapre datasets?
by
rpolicastro
12k
You should explain your experiment in more detail, such as the hypothesis you are testing and the samples you have to test this.
Comment: which statistical test and which package for comapre datasets?
by
satva72
• 0
thanks for you comment. I think its possible if we compare the different dataset?! to show that distribution is different between datasets.
Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra
by
Jeremy Leipzig
22k
seqr now supports Hail but with a layer of elasticsearch. It does not support TileDB but in theory it could.
Comment: which statistical test and which package for comapre datasets?
by
Jeremy
▴ 860
I think you will need at least three replicates to be able to do statistics.
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq
by
rpolicastro
12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq
by
RCMC
• 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
Traffic: 935 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