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121,147 results • Page
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0
votes
0
replies
11
views
error in reading codelink data
readcodelinkset
error
30 minutes ago by
nazaninhoseinkhan
▴ 530
0
votes
1
reply
74
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R
ChIP-seq
ENCODE
Diffbind
updated 2 hours ago by
Aspire
▴ 380 • written 8 hours ago by
stalo.lili
• 0
7
votes
5
replies
542
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
updated 4 hours ago by
cmdcolin
★ 4.2k • written 14 days ago by
Pierre Lindenbaum
166k
7
votes
5
replies
3.1k
views
News:
Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python
training
updated 5 hours ago by
Yue
• 0 • written 12.1 years ago by
Mary
11k
837
votes
170
replies
176k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 14 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
174
views
Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data
Breast-Cancer
TCGA
updated 12 hours ago by
Zhenyu Zhang
★ 1.3k • written 2 days ago by
BhagyashreeWaghale
• 0
0
votes
2
replies
185
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 19 hours ago by
GenoMax
151k • written 1 day ago by
bioinfo
▴ 150
0
votes
1
reply
173
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates
Omics
Pooling
updated 1 day ago by
ATpoint
88k • written 2 days ago by
sardius
• 0
0
votes
0
replies
104
views
Tool for Estimation of Purity and Ploidy in Precancerous Lesions
CNV
purity
genome
ploidy
1 day ago by
ting
• 0
8
votes
8
replies
590
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow
workflow
pipeline
1 day ago by
neng
▴ 30
0
votes
1
reply
155
views
What to choose as background in statistic test genetics
test
expression
gene
statistic
updated 1 day ago by
Dunois
★ 2.9k • written 1 day ago by
adigershon8897
• 0
1
vote
4
replies
365
views
differential exon usage from Salmon outputs
edgeR
diffSpliceDGE
DEU
salmon
updated 1 day ago by
Gordon Smyth
★ 7.9k • written 4 days ago by
n_navy
• 0
0
votes
0
replies
115
views
Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics
genetic-variation
epistasis
snp
gnomad
2 days ago by
SonicSoal
• 0
0
votes
0
replies
118
views
Rare variants association analysis (using WGS)
variant
GWAS
rare
WGS
2 days ago by
SeoG
• 0
0
votes
0
replies
130
views
Convert AnnData to Seurat (spatial transcriptomics, visium HD)
seurat
segmentation
anndata
visiumhd
updated 2 days ago by
GenoMax
151k • written 2 days ago by
npont
• 0
0
votes
0
replies
136
views
News:
Online course -Reproducibility in Bioinformatics - July 7–9
Singularity
Git
Docker
Snakemake
Nextflow
2 days ago by
Physalia-courses
★ 2.6k
1
vote
5
replies
391
views
RNA-Sequencing Analysis when control samples paired-end and tumour samples single-end
ENA
rna-sequencing
2 days ago by
h
• 0
0
votes
3
replies
283
views
STAR aligner - how is quality and correctness tested across builds/releases?
STAR
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Arthur
• 0
1
vote
2
replies
275
views
Pathway enrichment analysis on time-series data by filtering out age comparisons
pea
go
rnaseq
time-series
2 days ago by
fullycratered
• 0
4
votes
4
replies
322
views
building snpeff database for plant
plant
2 days ago by
analyst
▴ 60
1
vote
1
reply
194
views
How to find motif in specific region
motif
chip-seq
updated 3 days ago by
Alex Reynolds
36k • written 3 days ago by
zhang616123
• 0
0
votes
0
replies
172
views
How to interpret perplexing qcovhsp result in blastx
blastx
qcovhsp
blastn
2 days ago by
samuel.himes
• 0
0
votes
0
replies
148
views
Representation of GT:DS INFO tag for a missing marker in a VCF file
VCF
bcftools
3 days ago by
Mwangana
• 0
0
votes
0
replies
160
views
Best Practices for Integrating RNA-seq Time Series from Multiple Studies with Varying Protocols
differential-expression
meta-analysis
integration
RNA-seq
time-series
3 days ago by
enee
▴ 20
10
votes
9
replies
4.9k
views
bcftools query add header
bcftools
updated 3 days ago by
GenoMax
151k • written 3.1 years ago by
User000
▴ 750
0
votes
2
replies
319
views
Alternative to PASApipeline
transcriptomics
annotation
updated 2 days ago by
colindaven
7.4k • written 4 days ago by
lagartija
▴ 160
0
votes
0
replies
165
views
How to Get a Genetic Map, Given the Physical Position and Genotype Data of Markers
genetic-map
updated 3 days ago by
Ram
45k • written 3 days ago by
Daniyal
• 0
1
vote
7
replies
2.5k
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 4 days ago by
Michael
55k • written 2.4 years ago by
elizabeth
• 0
0
votes
2
replies
267
views
HISAT2 with Cleaned Data
HISAT2
RNASeq
1 day ago by
Gordonz9494
• 0
2
votes
1
reply
245
views
Definitions for "differential expression" and "differential abundance" in RNA-seq?
rna-seq
deseq
abundance
differential-expression
updated 3 days ago by
Ram
45k • written 4 days ago by
tw_140
• 0
2
votes
5
replies
387
views
Efficiently find regions in bed file that are within start and end regions of another bed file.
intersect
bedtools
updated 3 days ago by
Alex Reynolds
36k • written 4 days ago by
rxs1018
• 0
2
votes
4
replies
324
views
16S Libraries With Non-Purified Short Fragments
Sequencing
16S
Libraries
Magnetic
Beads
3 days ago by
alenew.am
▴ 10
0
votes
1
reply
248
views
How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
RNA-seq
cell
polyA
single
updated 4 days ago by
GenoMax
151k • written 4 days ago by
Ana
▴ 10
7
votes
6
replies
4.9k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2
ChIP-Seq
ChromHMM
MACS2
CHROMHMM
updated 4 days ago by
luminea
▴ 10 • written 5.9 years ago by
m.sadman.sakib
▴ 120
4
votes
5
replies
498
views
Editing and Adding to a GTF file
Annotation
Gene-ID
GTF
updated 3 days ago by
Ram
45k • written 6 days ago by
Keem Uarren Eiryll
▴ 10
4
votes
2
replies
269
views
Averaging multiple IgG BAM files for use as a control in ChromHMM
ChromHMM
bam
averag
updated 4 days ago by
ATpoint
88k • written 4 days ago by
luminea
▴ 10
3
votes
3
replies
477
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome
fastqc
shotgun
deduplication
updated 4 days ago by
colindaven
7.4k • written 9 days ago by
vikasmh111
• 0
0
votes
0
replies
185
views
News:
online course: Introduction to Genome Annotation
Gene-Prediction
Genome-Annotation
Gene-Models
4 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
1.2k
views
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module
concoct
metawrap
module
4 days ago by
shevch2009
• 0
2
votes
7
replies
475
views
Circular heatmap using circos.heatmap in R
R
circos
heatmap
circularheatmap
updated 3 days ago by
GenoMax
151k • written 5 days ago by
Yukta
• 0
0
votes
0
replies
215
views
Zebrafish phenotype ontology enrichment analyses
ontology
zebrafish
5 days ago by
Li
• 0
0
votes
2
replies
302
views
Sequence Duplication for Single-End 3RAD Data
duplication
reduced-representation
4 days ago by
Sarah
• 0
0
votes
0
replies
219
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
5 days ago by
Adrian
• 0
1
vote
6
replies
1.1k
views
6 follow
Not retrieving Mitochondrial Genes in Single Cell analysis
single-cell
updated 5 days ago by
Ram
45k • written 10 months ago by
guioliveirareis
▴ 10
0
votes
0
replies
213
views
News:
Ancient Metagenomics course - online, May 27-29
ancient-metagenomics
aDNA
aMeta
5 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
263
views
Issues running scAPAtrap
scAPAtrap
polyA
scRNAseq
updated 5 days ago by
GenoMax
151k • written 5 days ago by
Ana
▴ 10
5
votes
3
replies
372
views
What are BED files?
BED
updated 5 days ago by
Alex Reynolds
36k • written 5 days ago by
Besoa
• 0
3
votes
8
replies
563
views
ggplot make boxplots more wide
ggplot2
r
5 days ago by
Nona
▴ 90
2
votes
1
reply
321
views
Minimum number of samples for multi-omics data integration
multi-omics
updated 5 days ago by
Ram
45k • written 6 days ago by
Tundup
▴ 10
1
vote
0
replies
255
views
News:
Workshop: Virtual Genome Annotation, May 27–29
GenomeAnnotation
workshop
UConn
6 days ago by
zsc25001
▴ 10
121,147 results • Page
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Recent Votes
Answer: No variant in the Pseudoautosomal regions of gomad chrY ?
Answer: Efficiently find regions in bed file that are within start and end regions of an
Answer: Efficiently find regions in bed file that are within start and end regions of an
Answer: Why GATK4 doesn't carry out local realignment around indels ?
Answer: How do you generate TMM normalized counts using EdgeR?
Answer: How do you generate TMM normalized counts using EdgeR?
Answer: How do you generate TMM normalized counts using EdgeR?
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nazaninhoseinkhan
▴ 530
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Recent Replies
Answer: DiffBind analysis with ENCODE data using R and .bed/.bam files
by
Aspire
▴ 380
> most examples assume FASTQ-level input Perhaps the reason for this impression is looking in ENCODE pipelines&workflows. But take a look…
Answer: No variant in the Pseudoautosomal regions of gomad chrY ?
by
cmdcolin
★ 4.2k
On the UCSC hg19 genome, the PAR regions on Y are actually exact copies of X This is described here ``` The Y chromosome in this assembl…
Answer: Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming
by
Yue
• 0
i would like to attend, but the website is NOT FOUND
Answer: Selecting clinical rows for repeated case IDs in TCGA-BRCA data
by
Zhenyu Zhang
★ 1.3k
I assume you downloaded the data from GDC. First, GDC has a very helpful help desk support@nci-gdc.datacommons.io you can ask. Secondly, I …
Comment: Kallisto to tximport to deseq2
by
bioinfo
▴ 150
Thank you so much for replying. Would you do the paste instead of tximport? When I use biomart I specify the version I want to use to make …
Answer: Kallisto to tximport to deseq2
by
ATpoint
88k
I would always do either gene_id or `paste(gene_id, gene_name, sep = "_")` because gene_name has duplicates, which can cause conflicts. Gen…
Answer: Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness
by
ATpoint
88k
Without further details I would recommend against doing unreplicated experiments as replication is key for any meaningful pairwise statisti…
Comment: What to choose as background in statistic test genetics
by
Dunois
★ 2.9k
The background should be the set of all genes that are common to both tissues. The foreground is the set of "significant" genes (e.g., base…
Comment: HISAT2 with Cleaned Data
by
Gordonz9494
• 0
Hi, Thank you for your comment. Regarding your question about the "counts are too low," I’m working with the cleaned data provided by th…
Answer: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
neng
▴ 30
Ok, I finally find the solution. I would like to share with you guys: workflow { // Step 7: split SplitFasta(params.fasta)…
Answer: differential exon usage from Salmon outputs
by
Gordon Smyth
★ 7.9k
If you want to detect differential splicing using edgeR with Salmon output, then you should do DTU instead of DEU, see: Baldoni PL#, Chen …
Comment: Nextflow: split a FASTA file into 5 parts to enable parallel processing
by
neng
▴ 30
Yeah, it's a good solution I've tried. The only problem is that the SplitFasta() process has to be finished before it starts, otherwise it …
Comment: differential exon usage from Salmon outputs
by
dsull
★ 7.5k
Providing each exon as an individual transcript will throw off pseudoalignment-type algorithms which assume that each read originated from …
Comment: Create local Blast database alias with blastdb_aliastool fails
by
GenoMax
151k
Can you set the following variable and see if that helps. BLASTDB=f:/BlastDB/nr/nr export BLASTDB
Comment: building snpeff database for plant
by
analyst
▴ 60
Is it safe to add -noCheckCds -noCheckProtein in the command or will it skip important information in the resultant database: java -Xm…
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