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104,035 results • Page
1 of 2081
Sort: Rank
Rank
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Votes
Replies
0
votes
0
replies
6
views
Generate consensus sequence without considering gaps
seqinr
R
consensus
fasta
7 minutes ago by
Nathan
▴ 10
0
votes
0
replies
9
views
Ensembl, Fetch "Phenotypes" information
Ensembl
1 hour ago by
hmende.z
• 0
0
votes
0
replies
10
views
Has anybody managed to install and run GroopM lately?
metagenomics
groopM
binning
1 hour ago by
JohnVollmers
• 0
0
votes
1
reply
21
views
Accessing gene names from an Affymetrix GeneFeatureSet
R
Affymetrix
Microarray
GEO
updated 1 hour ago by
GenoMax
118k • written 2 hours ago by
Bryan
• 0
0
votes
3
replies
181
views
feature counts invalid parameter
invalid
feature
counts
parameter
updated 1 hour ago by
Ram
36k • written 15 days ago by
smithkthedale
▴ 10
0
votes
0
replies
30
views
How to split GWAS data into two parts using Plink
plink
GWAS
3 hours ago by
davidenoma
▴ 50
0
votes
3
replies
897
views
Extracting assembly accession number and protein ID using e-utilities
sequence
assembly
genome
e-utilities
updated 3 hours ago by
GenoMax
118k • written 2.8 years ago by
geizetomazetto
• 0
2
votes
3
replies
71
views
Adding @RG header line to bam and sam files in hisat2
bam
hisat2
header
alignment
updated 2 hours ago by
Jeremy
▴ 510 • written 4 hours ago by
Nemo
• 0
0
votes
1
reply
49
views
Trouble Running MrBayes with GPU(s)
phylogenetics
MrBayes
Bayesian
GPU
inference
updated 4 hours ago by
Mensur Dlakic
★ 20k • written 5 hours ago by
rosslindsey1
• 0
1
vote
6
replies
258
views
GATK's selectVariants not outputting VCF
GATK
5 hours ago by
dec986
▴ 340
4
votes
10
replies
158
views
Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
Institute
ftp
Broad
gatk
updated 4 hours ago by
Ram
36k • written 6 hours ago by
appropiate
▴ 30
0
votes
1
reply
49
views
Installing ensembl-vep
vep
ensembl-vep
updated 1 hour ago by
Ram
36k • written 6 hours ago by
maajid
• 0
688
votes
160
replies
92k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 3 months ago by
Biostar
960 • written 5.7 years ago by
Istvan Albert
94k
0
votes
0
replies
28
views
Loading a pre-filtered loom file into pySCENIC
pySCENIC
scRNA
seq
loom
file
7 hours ago by
Jacob
• 0
1
vote
1
reply
45
views
Filtering multiple-samples VCF by genotype with GATK
GATK
SNPs
updated 7 hours ago by
LChart
▴ 380 • written 7 hours ago by
Timotheus
▴ 10
0
votes
0
replies
33
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
Computation
wateRmelon
EPIC
minfi
DNA
methylation
7 hours ago by
calen.p.ryan
• 0
0
votes
1
reply
76
views
RNAseq matrix input for WGCNA analysis
WGCNA
updated 7 hours ago by
LChart
▴ 380 • written 8 hours ago by
cardon.chc
• 0
2
votes
1
reply
85
views
How to get intersected variants between multiple vcf files?
vcftools
intersection
gatk
isec
bcftools
updated 6 hours ago by
Jeremy Leipzig
20k • written 11 hours ago by
Dana
▴ 10
3
votes
2
replies
65
views
How to check Burrows-Wheeler Aligner (BWA) version on my terminal?
BWA
aligner
7 hours ago by
appropiate
▴ 30
1
vote
2
replies
76
views
Why are reads from a region of a gene but not recongined as a mapped reads>
bam
nanopore
alignment
samtools
updated 3 hours ago by
Pierre Lindenbaum
147k • written 7 hours ago by
BenBoErBa
▴ 10
0
votes
0
replies
30
views
How to generate gene body coverage plot for tRNA?
clipseq
RNAseq
peakcalling
samtools
8 hours ago by
barrypraveen
▴ 40
2
votes
2
replies
87
views
Primer3_core
line
command
Primer3_core
updated 9 hours ago by
GenoMax
118k • written 10 hours ago by
Mohamed
• 0
0
votes
4
replies
96
views
error in kmergenie compilation
kmergenie
ntcard
error
updated 9 hours ago by
GenoMax
118k • written 10 hours ago by
Shakunthala Natarajan
• 0
0
votes
0
replies
49
views
High proportion of non-biallelic SNPs in dbSNP 155 vs 144
sumstats
dbSNP
Bioinformatics
GWAS
genetics
10 hours ago by
Al Murphy
▴ 30
0
votes
0
replies
35
views
Conversion of h5Seurat to h5ad with SeuratDisk
scRNA
bioinformatics
SeuratData
Seurat
SeuratDisk
10 hours ago by
c2e09af0
• 0
0
votes
1
reply
70
views
How to download a locked sra file from NCBI SRA?
SRA
FASTQ
Locked
updated 10 hours ago by
GenoMax
118k • written 11 hours ago by
sabreenaalam12345
• 0
0
votes
1
reply
65
views
Pilercr ***FATAL ERROR*** help
programming
pilercr
bioinformatics
updated 10 hours ago by
GenoMax
118k • written 11 hours ago by
116439372
• 0
0
votes
0
replies
42
views
News:
Online training -Getting the most out of R
R
Science
analysis
Data
11 hours ago by
carlopecoraro2
★ 2.1k
0
votes
0
replies
41
views
Allele Frequency using different kits versions: Agilent SureSelect Human All Exon V4 and V5
Agilent
SureSelect
allele
frequency
version
11 hours ago by
m.bamajboor
• 0
0
votes
4
replies
126
views
Sudden drop in coverage in single-cell RNA-sequencing data
singlecell
6 hours ago by
tien
▴ 10
0
votes
0
replies
42
views
News:
Online training - Cancer Genomics in R
Bioinformatics
Genomics
Cancer
R
12 hours ago by
carlopecoraro2
★ 2.1k
4
votes
2
replies
172
views
Modelling vs removing effects from confounding variables and their uses for downstream analyses in RNA-seq experiments
removebatcheffect
sva
heatmap
plot
limma
pca
updated 12 hours ago by
Vincent Laufer
★ 2.2k • written 15 hours ago by
Jasmin
▴ 10
1
vote
1
reply
76
views
A method to find if a variant is Genomic or an RNA-Editing variant
Editing
RNA-Seq
WES
RNA
Variant
updated 13 hours ago by
i.sudbery
15k • written 14 hours ago by
hkarakurt
▴ 150
0
votes
1
reply
78
views
How to match tumor fastq file to normal fastq file? (I just have a set of tumor data and another set of normal data)
WholeExomeSequencing
NextGenerationSequencing
updated 15 hours ago by
tomas4482
▴ 280 • written 16 hours ago by
Joshua
• 0
0
votes
0
replies
45
views
BEDOPS convert2bed output
vcf
bedops
convert2bed
bed
15 hours ago by
nehaklkn
• 0
4
votes
4
replies
219
views
Are upset plots bad for differential expression analysis?
shiny
ComplexUpset
differential
expression
R
upset
6 hours ago by
paulimer
▴ 10
2
votes
4
replies
148
views
Distinguishing records for reads in a pair in a SAM file
SAM
sequencing
14 hours ago by
appropiate
▴ 30
1
vote
2
replies
198
views
Circos plot from SV data of WES samples
Circos
SV
plot
updated 17 hours ago by
d-cameron
★ 2.6k • written 6 days ago by
Hasib
▴ 10
0
votes
2
replies
92
views
How to calculate position-specific fastq stats?
rnaseq
fastq
metagenomics
genomics
6 hours ago by
O.rka
▴ 620
1
vote
0
replies
48
views
Finding Specific Types of Data for Cancer Studies
TCGA
GDC
Cancer
Entrez
GEO
19 hours ago by
Vincent Laufer
★ 2.2k
1
vote
2
replies
151
views
How to check fastq file for feature retained from vector construct after RNA-seq
RNA
sequencing
fastq
vector
updated 19 hours ago by
Zhenyu Zhang
▴ 560 • written 1 day ago by
soup
• 0
1
vote
3
replies
304
views
TCGA RNA-Seq data and CLINICAL Data
rna-seq
barcode
clinical
gdc
tcga
updated 19 hours ago by
Zhenyu Zhang
▴ 560 • written 4 weeks ago by
albacaro
• 0
0
votes
1
reply
139
views
Different types of imagery data available in TCGA
TCGA
images
slide
tissue
wholes
diagnostic
updated 19 hours ago by
Zhenyu Zhang
▴ 560 • written 4 weeks ago by
kountaydwivedi
• 0
0
votes
0
replies
85
views
Should the repressor really have a negative correlation with its motif?
atac-seq
scatac-seq
single-cell
9 hours ago by
Janus
• 0
0
votes
1
reply
115
views
CPTAC data, download, merge
CPTAC
merging
seq
data
RNA
updated 19 hours ago by
Zhenyu Zhang
▴ 560 • written 8 days ago by
Rob
▴ 130
1
vote
0
replies
80
views
How does LUMPY report breakpoints in multiple samples?
lumpy
SV
breakpoint
variation
structural
SVs
23 hours ago by
Getting there
▴ 80
10
votes
14
replies
440
views
7 follow
AF = 0.5 in chrX, VCF of a male
VCF
AF
chrX
9 hours ago by
paolo
▴ 10
2
votes
1
reply
130
views
Convert RPKM into Counts
gene
data
r
expression
updated 23 hours ago by
abbey
▴ 210 • written 1 day ago by
Dhruv
▴ 10
1
vote
2
replies
123
views
Conda environment perl issue
perl
synima
python
conda
9 hours ago by
Paulo
• 0
0
votes
1
reply
99
views
Getting coordinates of unmapped regions and regions that map to them
reference
genome
unmapped
regions
updated 1 day ago by
Istvan Albert
94k • written 1 day ago by
ja569116
• 0
104,035 results • Page
1 of 2081
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Answer: R ggplot stacked histogram - how to plot the small proportion on top (or color l
Comment: SQL query to find all specific value in all columns based on row id.
A: Extraction of first sequences from a big fasta file
Extraction of first sequences from a big fasta file
Extraction of first sequences from a big fasta file
Comment: Adding @RG header line to bam and sam files in hisat2
Answer: Adding @RG header line to bam and sam files in hisat2
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Comment: R ggplot stacked histogram - how to plot the small proportion on top (or color l
by
Bianca
• 0
Hi @zepper! That was a great advice, thanks!
Comment: set-all-var-ids misuse in plink 2.0
by
hi.there
• 0
Thank you. So I have isolated the chromosome, rsids and chromosome positions from the original bim file into its own file (I'm not sure if…
Answer: Accessing gene names from an Affymetrix GeneFeatureSet
by
GenoMax
118k
You can find the gene names in the `platform` files (that contain annotation) for this chip: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi…
Comment: feature counts invalid parameter
by
Ram
36k
Do not add answers unless you're answering the top level question. Use `Add Comment` or `Add Reply` instead. I'm moving your post to a comm…
Comment: feature counts invalid parameter
by
Ermin
• 0
I have the same error, is this a software installation issue? ``` docker run -v /input/:/input -v 6.amazonaws.com/bioinfo-notebooks /roo…
Comment: Tools for finding the duplications in genomes for phylogenomics study ?
by
pinn
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Orthofinder, Orthoscope, blastp all vs. all.
Comment: Zenodo command line uploads
by
Arup Ghosh
3.0k
Zenodo developer page has a python and cURL implementation of their REST API. https://developers.zenodo.org/?python#quickstart-upload
Comment: Adding @RG header line to bam and sam files in hisat2
by
Jeremy
▴ 510
If you don't want to rerun the alignment, you can use picard AddOrReplaceReadGroups. However, GATK recommends adding read groups at the al…
Comment: Extract nucleotide sequence from a RefSeq Transcript ID
by
GenoMax
118k
How about (truncated for space). First columns is rsID. $ esearch -db nuccore -query NM_001346941 | elink -target gene | elink -target…
Comment: Installing ensembl-vep
by
Arup Ghosh
3.0k
VEP requires Archive::Zip and DBI Perl modules, install them using `cpanm`. More details regarding dependencies are available in the instal…
Comment: Why are reads from a region of a gene but not recongined as a mapped reads>
by
Pierre Lindenbaum
147k
can you please show us the **full** ouput of `samtools view your.bam '5:3056998-3063970'`
Answer: Extracting assembly accession number and protein ID using e-utilities
by
GenoMax
118k
Using [**EntrezDirect**][1]: $ more id VUX63899.1 QDO61010.1 QDO50771.1 Since `epost` method does not keep track o…
Comment: Extract nucleotide sequence from a RefSeq Transcript ID
by
Vincent Laufer
★ 2.2k
Looks like this does a lot of it?? https://github.com/zwdzwd/transvar
Comment: Extract nucleotide sequence from a RefSeq Transcript ID
by
Vincent Laufer
★ 2.2k
Hey Geno!! Sure. thanks so much for following up. Suppose what I have is: NM_001346941 p.N550H .. but what I want is: …
Comment: Extracting assembly accession number and protein ID using e-utilities
by
geizetomazetto
• 0
Hi Morgan, Yes, I did. Thanks. Best,
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