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113,964 results • Page
1 of 2280
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
92
views
Need help to find FASTA sequence from dbSNP
dbSNP
SNP
FASTA
51 minutes ago by
syedahumairagillani
• 0
2
votes
3
replies
170
views
Calculate GC content for entire chromosome
bam
GC
assembly
bwa-mem
updated 57 minutes ago by
colindaven
5.8k • written 17 hours ago by
skilleta0527
• 0
0
votes
1
reply
23
views
Execute R command on specific termimal
R
script
terminal
updated 1 hour ago by
ATpoint
78k • written 1 hour ago by
QX
• 0
1
vote
1
reply
116
views
How to use Nextflow to call scripts from different environments?
wrapper
environments
anaconda
conda
nextflow
updated 3 hours ago by
ATpoint
78k • written 12 hours ago by
O.rka
▴ 710
0
votes
0
replies
44
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
6 hours ago by
junhuili
• 0
1
vote
5
replies
786
views
Strandedness of RNA-seq results
dual-RNA-seq
featurecounts
strandedness
HISAT2
updated 5 hours ago by
charles.feigin
• 0 • written 18 months ago by
jamesymtang
▴ 10
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
1
vote
1
reply
971
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 5 hours ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
51
views
megablast taxonomy assign in blobtools
blobtools
8 hours ago by
bs
• 0
0
votes
0
replies
65
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
11 hours ago by
George X.
• 0
0
votes
1
reply
97
views
Cell ranger multi for demultiplexing FB files and GEX files
ranger
multi
cell
updated 8 hours ago by
GenoMax
136k • written 12 hours ago by
Shloka
• 0
0
votes
0
replies
61
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
14 hours ago by
EK
• 0
0
votes
1
reply
105
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
9 hours ago by
LauferVA
3.8k
4
votes
15
replies
6.3k
views
8 follow
bbmap split paired-end reads back into separated fastq files?
genome
next-gen-sequencing
bbmap
alignment
updated 8 hours ago by
GenoMax
136k • written 5.2 years ago by
c.e.chong
▴ 60
0
votes
1
reply
126
views
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException
phg
updated 16 hours ago by
lcj34
▴ 250 • written 21 hours ago by
ryan
• 0
1
vote
1
reply
104
views
ANNOVAR Download Failing
ANNOVAR
updated 14 hours ago by
Ram
41k • written 17 hours ago by
tony
• 0
0
votes
1
reply
113
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 14 hours ago by
Ram
41k • written 17 hours ago by
mgranada3
▴ 30
0
votes
2
replies
159
views
Downsampling ATAC-seq BAM files
ATAC-seq
13 hours ago by
Elise
• 0
0
votes
0
replies
63
views
spatial metabolomics, python
spatial-metabolomics
updated 18 hours ago by
Ram
41k • written 18 hours ago by
joha
▴ 10
0
votes
3
replies
298
views
RNA seq
Differential-gene-expression
updated 18 hours ago by
jv
★ 1.3k • written 2 days ago by
Byonkesh
• 0
0
votes
4
replies
411
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
updated 18 hours ago by
Ram
41k • written 4 days ago by
fluke
• 0
1
vote
4
replies
174
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 5 hours ago by
GenoMax
136k • written 20 hours ago by
Javier
• 0
0
votes
0
replies
78
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
20 hours ago by
kdca
• 0
0
votes
2
replies
150
views
Issues while running blastx
blastx
RNA-seq
updated 5 hours ago by
GenoMax
136k • written 23 hours ago by
Foad
▴ 10
0
votes
1
reply
105
views
Tophat2 Error running 'long_spanning_reads' on M1 Mac
Tophat2
Boost
RiboSeq
M1-Mac
updated 18 hours ago by
Ram
41k • written 22 hours ago by
riboseq938
• 0
0
votes
1
reply
137
views
Contrasts in R
contrasts
r
updated 18 hours ago by
jv
★ 1.3k • written 22 hours ago by
SGMS
▴ 130
1
vote
5
replies
616
views
ATAC-Seq and RPKM
RPKM
ATAC-Seq
updated 21 hours ago by
ATpoint
78k • written 9 weeks ago by
qudrat.nii
• 0
0
votes
1
reply
1.3k
views
Correlation RNA-seq and ATAC-seq
RNA-Seq
R
gene
updated 22 hours ago by
Tao Zhu
▴ 10 • written 3.4 years ago by
pastel950818
• 0
5
votes
4
replies
851
views
Methods to integrate ATAC-seq and RNA-seq
RNA-seq
ATAC-seq
updated 22 hours ago by
Tao Zhu
▴ 10 • written 4 months ago by
Chris
▴ 230
0
votes
1
reply
114
views
Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release
bcftools
dbSNP
tabix
vcf
updated 18 hours ago by
Ram
41k • written 22 hours ago by
Fernando
• 0
0
votes
1
reply
299
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 22 hours ago by
Joe
21k • written 23 hours ago by
Ralph
• 0
1
vote
2
replies
157
views
contrast file in DESeq2 bioconductor
DEseq2
updated 18 hours ago by
Ram
41k • written 23 hours ago by
r.shiasi3897
▴ 10
1
vote
2
replies
270
views
Best method for batch correction of three datasets
RNA-seq
updated 3 hours ago by
ATpoint
78k • written 1 day ago by
CTLong
▴ 20
0
votes
1
reply
122
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 18 hours ago by
Ram
41k • written 23 hours ago by
francesco.degiglio
• 0
0
votes
0
replies
82
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
1 day ago by
sil_bioinfo
▴ 40
0
votes
0
replies
71
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
1 day ago by
Saad Khan
▴ 420
0
votes
0
replies
70
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
1 day ago by
Adrian
• 0
1
vote
7
replies
267
views
How to download multiple genome files using command line (MacOS) using datasets
ncbi-datasets
Bacteria
Genome
updated 15 hours ago by
Ram
41k • written 1 day ago by
scholaraspect2008
• 0
3
votes
1
reply
130
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 18 hours ago by
Ram
41k • written 1 day ago by
Confused_human
▴ 20
0
votes
3
replies
174
views
Microarray batch correction method suggestions
microarray
batch-correction
updated 14 hours ago by
Ram
41k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
82
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
1 day ago by
Clayton
• 0
0
votes
0
replies
85
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 18 hours ago by
Ram
41k • written 1 day ago by
Maatary
• 0
2
votes
1
reply
159
views
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
transcript_reads
updated 1 day ago by
Jeremy
▴ 860 • written 1 day ago by
Faith
▴ 40
2
votes
2
replies
156
views
Help with gatk CreateSequenceDictionary
GATK
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Chris
▴ 230
2
votes
5
replies
338
views
FastQC without yellow box
fastqc
updated 18 hours ago by
Ram
41k • written 1 day ago by
lobelino
• 0
0
votes
1
reply
139
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 1 day ago by
Brian Bushnell
20k • written 1 day ago by
isMM
• 0
2
votes
4
replies
242
views
error when installing gistic2 using conda
conda
gistic2
updated 14 hours ago by
Ram
41k • written 1 day ago by
luckyday1661
• 0
0
votes
0
replies
103
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 1 day ago by
Ram
41k • written 1 day ago by
boone5jones
• 0
0
votes
0
replies
89
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
1 day ago by
S
• 0
3
votes
2
replies
242
views
RNA-seq log2 fold change to linear
RNA-seq
DGE
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
hmiller
• 0
113,964 results • Page
1 of 2280
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Answer: How to use Nextflow to call scripts from different environments?
Comment: An issue with gtf file (ballgownrsem)
Answer: how to calculate duplicated reads in single cell RNA 10x genomics data
What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
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Recent Replies
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
• 0
Thank you for your response. Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
Answer: Calculate GC content for entire chromosome
by
colindaven
5.8k
In the meantime there is also seqtk gc https://github.com/lh3/seqtk seqtk gc Usage: seqtk gc [options] <in.fa> …
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
I have employed your above suggested approach for BQSR (latter one). I will try former approach too (that does not require reference vcf fi…
Comment: An issue with gtf file (ballgownrsem)
by
cucindarko51
• 0
Thank you! After using this tool, I figured out that **ballgownrsem** can be run successfully only with GFF files.
Answer: Execute R command on specific termimal
by
ATpoint
78k
This is not how HPCs work. Things do not happen automatically and independent of the job scheduler. If you want to work interactively o…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Using [**EntrezDirect**][1] you can find the location of this SNP: $ esearch -db snp -query rs1815739 | esummary | xtract -pattern Doc…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
For variant calling I followed following steps: **Step 1** I first made a vcf file to be used for quality score recalibration later > c…
Comment: Need help to find FASTA sequence from dbSNP
by
Pierre Lindenbaum
158k
what does it mean ?
Answer: How to use Nextflow to call scripts from different environments?
by
ATpoint
78k
You can specify conda environments and containers directly in the modules, see for example: https://github.com/nf-core/modules/blob/master…
Comment: Issues while running blastx
by
GenoMax
136k
> ~/Downloads/uniprot_sprot.dat `dat` files are not blast index ready. You should download the `fasta` format file and create your own bla…
Comment: Strandedness of RNA-seq results
by
charles.feigin
• 0
Hi, coming here for the same reason. Libraries prepared with the Illumina Stranded mRNA Prep kit (dUTP-based). In hisat2 with --rf I get <…
Comment: How to interpret the discrepancy of assignment rate in featurecounts using forwa
by
charles.feigin
• 0
I'm having this exact same problem. PolyA RNA-Seq library, running with --fr in hisat2 gives a high fraction of concordant single-mappers, …
Comment: How to create a mutation frequency comparison plot?
by
saipra003
▴ 10
That's awesome thank you. Found out after a bit of researching that this is called a `Cleveland Dot Plot` if anyone else comes across this.
Comment: Cell ranger multi for demultiplexing FB files and GEX files
by
GenoMax
136k
Demultiplexing is typically done using Illumina software? Have you done this already?: https://www.10xgenomics.com/support/software/cell-ra…
Comment: bbmap split paired-end reads back into separated fastq files?
by
GenoMax
136k
If you simply want to merge "technical" sequencing replicates then you can do the following cat file1_R1.fastq file1_R1.fastq > merged…
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