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
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
221
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 14 days ago by
GenoMax
142k • written 14 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
334
views
Correlation Analysis
statistics
methylation
NGS
expression
10 days ago by
Researcher
▴ 30
1
vote
2
replies
214
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
14 days ago by
robert.flynn.21
• 0
0
votes
0
replies
133
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
14 days ago by
Scott McKay
▴ 30
0
votes
0
replies
117
views
Cellphonedb results
cpdb
visulization
cellphonedb
14 days ago by
piotto
▴ 20
0
votes
0
replies
130
views
Cox Model with interaction item interpretation
Cox
15 days ago by
Bine
▴ 60
0
votes
0
replies
119
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
12 days ago by
Javier
• 0
1
vote
7
replies
584
views
Question regarding WGCNA
WGCNA
Network-construction
12 days ago by
deepak
• 0
0
votes
0
replies
118
views
vdjtools
vdjtools
15 days ago by
yueli7
▴ 250
0
votes
1
reply
319
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 14 days ago by
andres.firrincieli
3.6k • written 15 days ago by
Antonio
• 0
0
votes
0
replies
132
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 15 days ago by
Ram
44k • written 15 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
115
views
Normalizing AMR gene count data
abundance
RGI
updated 15 days ago by
Ram
44k • written 15 days ago by
arshad1292
▴ 100
1
vote
1
reply
195
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 5 days ago by
Jordan M Eizenga
▴ 460 • written 15 days ago by
sarumonsus
▴ 10
0
votes
0
replies
138
views
How to implement an IGV to streamlit app?
python
streamlit
igv
15 days ago by
avigail.shnaider
• 0
0
votes
0
replies
141
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
16 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
132
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
16 days ago by
Christopher
• 0
0
votes
0
replies
133
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
16 days ago by
DGTool
▴ 20
2
votes
3
replies
369
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 12 days ago by
bk11
★ 2.5k • written 16 days ago by
Yoosef
▴ 60
0
votes
1
reply
288
views
creating batch colum for batch correction
batch-correction
combat
15 days ago by
Expert
▴ 10
0
votes
1
reply
250
views
Help with DGEList function
DGEList
R
updated 15 days ago by
marco.barr
▴ 130 • written 17 days ago by
Natali
• 0
0
votes
0
replies
173
views
Homer motif analysis
Homer
17 days ago by
daffodil
▴ 10
0
votes
2
replies
288
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 11 days ago by
GenoMax
142k • written 17 days ago by
Ximena
• 0
0
votes
1
reply
228
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 17 days ago by
Ram
44k • written 17 days ago by
Valentina
• 0
0
votes
6
replies
506
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 17 days ago by
swbarnes2
14k • written 18 days ago by
Erina
• 0
1
vote
3
replies
348
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
16 days ago by
Lada
▴ 30
1
vote
0
replies
164
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 15 days ago by
zx8754
11k • written 18 days ago by
Emilie
▴ 10
0
votes
0
replies
152
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
18 days ago by
Javier
• 0
0
votes
2
replies
321
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 8 days ago by
Zhenyu Zhang
★ 1.2k • written 18 days ago by
yahn
• 0
0
votes
0
replies
147
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
18 days ago by
mikemakaveli1
• 0
2
votes
2
replies
259
views
Raw counts using stringtie
stringtie
RNA-seq
updated 18 days ago by
GenoMax
142k • written 18 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
142
views
Modify plot R mtDNA indel
plot
mtDNA
R
18 days ago by
marco.barr
▴ 130
0
votes
0
replies
344
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
18 days ago by
NorbertK
▴ 10
0
votes
2
replies
295
views
Downloading older version of a tool
Alignment
tools
17 days ago by
Ruqaiya
• 0
0
votes
0
replies
165
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
18 days ago by
rustykb
▴ 20
3
votes
5
replies
359
views
Generating mpileup file using samtools
mpileup
samtools
updated 18 days ago by
Joe
21k • written 18 days ago by
Ruqaiya
• 0
2
votes
3
replies
344
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 18 days ago by
dthorbur
★ 2.0k • written 18 days ago by
Vijith
▴ 30
0
votes
0
replies
167
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
18 days ago by
Jeyong
• 0
0
votes
0
replies
157
views
Empty table plot using plotGseaTable()
FGSEA
17 days ago by
Chris
▴ 280
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 19 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
253
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
19 days ago by
dtnondorf
• 0
3
votes
8
replies
644
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
15 days ago by
Qroid
▴ 40
0
votes
1
reply
193
views
Provean help
variant
Provean
updated 19 days ago by
Mensur Dlakic
★ 27k • written 19 days ago by
Arun Sai Kumar
• 0
0
votes
0
replies
118
views
Use of annotation of integrated Seurat object in single sample
Seurat
19 days ago by
Bine
▴ 60
0
votes
1
reply
270
views
Subsetting and merging back Seurat Object brings different results
Seurat
19 days ago by
Bine
▴ 60
1
vote
1
reply
176
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 19 days ago by
Ram
44k • written 19 days ago by
marco.barr
▴ 130
0
votes
0
replies
115
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
19 days ago by
Vijith
▴ 30
0
votes
0
replies
122
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
19 days ago by
James
▴ 10
0
votes
1
reply
615
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 19 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
1
vote
3
replies
305
views
Odd alignment question/finding
Alignment
updated 18 days ago by
barslmn
★ 2.2k • written 19 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
244
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 19 days ago by
GenoMax
142k • written 19 days ago by
mgranada3
▴ 30
1,000 results • Page
4 of 20
Recent Votes
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Recent Locations •
All
United States,
just now
Santiago,
just now
Canada,
1 minute ago
Brazil,
2 minutes ago
United States,
2 minutes ago
United Kingdom,
3 minutes ago
United States,
4 minutes ago
Recent Awards •
All
Scholar
to
Ashutosh Pandey
12k
Student
to
Holly
▴ 30
Popular Question
to
O.rka
▴ 720
Popular Question
to
natasha.sernova
★ 4.0k
Popular Question
to
Picasa
▴ 640
Supporter
to
Mol
• 0
Popular Question
to
Rafael Soler
★ 1.2k
Recent Replies
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Ram
44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
Comment: Multiplexing for pooled CRISPR screen sequencing
by
GenoMax
142k
> If we switch to pair-end sequencing with dual-index barcode You can use dual-indexing with single end reads. You don't need to do paired…
Comment: Super ehancers
by
jared.andrews07
★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
finch
• 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Traffic: 3075 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