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119,597 results • Page
1 of 2392
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0
votes
1
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37
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making estimated proteome from genome
NCBI
updated 2 hours ago by
GenoMax
147k • written 2 hours ago by
dec986
▴ 380
0
votes
0
replies
31
views
Can anyone help me with this script error?
GSVA
updated 2 hours ago by
GenoMax
147k • written 3 hours ago by
nuorain
▴ 30
1
vote
2
replies
147
views
Combine GBS and WGS data for variant calling in GWAS analysis
GBS
Combined
WGS
20 minutes ago by
behnam
▴ 10
0
votes
0
replies
50
views
Job:
Job Opening - Post-Doctoral Research Fellow - Cancer Immunotherapy
systems-biology
immunology
protein-engineering
research-fellow
postdoc
updated 6 hours ago by
Ram
44k • written 7 hours ago by
Fred Hutch (Recruiting)
▴ 20
0
votes
0
replies
48
views
Computational tools for predicting novel substrates for a class of enzymes
substrate
catalysis
enzyme
8 hours ago by
yarrowmadrona
▴ 10
1
vote
4
replies
184
views
How to include the lane index in STARsolo count matrix barcodes.tsv?
10x
starsolo
singlecell
star
alignment
updated 5 hours ago by
swbarnes2
14k • written 1 day ago by
mk
▴ 300
0
votes
2
replies
426
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
seurat
scRNA-seq
miloR
updated 10 hours ago by
michael.morgan
• 0 • written 6 months ago by
shuaizh117
▴ 10
820
votes
169
replies
159k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
3.1k • written 8.0 years ago by
Istvan Albert
101k
0
votes
2
replies
110
views
How to Identify Strain-Specific HPV and EBV Integration Sites in Human Whole Genome Sequencing Data?
ebv
hpv
genomics
updated 10 hours ago by
GenoMax
147k • written 11 hours ago by
adam
• 0
2
votes
3
replies
211
views
Can I combine variants called using T2T-CHM13 with GRCh38?
chm13
t2t-chm13
updated 11 hours ago by
Jeremy Leipzig
22k • written 3 days ago by
Rina
▴ 20
3
votes
2
replies
148
views
Getting gnomAD allele frequencies for checking against populations
gnomAD
ancestry
allele-frequency
updated 11 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
Peter
▴ 10
2
votes
1
reply
123
views
Using reference genome for GSEA for different strains of the same bacterial species
RNAseq
GSEA
updated 12 hours ago by
Istvan Albert
101k • written 1 day ago by
Texx
▴ 20
0
votes
3
replies
129
views
lncRNA and mRNA analysis on Total RNA Sequencing data
mRNA
RNASeq
lncRNA
updated 12 hours ago by
Istvan Albert
101k • written 14 hours ago by
kanika.151
▴ 160
0
votes
0
replies
53
views
News:
Course: Structural Variant Bioinformatics
Long-Reads
Nanopore
PacBio
Structural-Variations
updated 12 hours ago by
Ram
44k • written 13 hours ago by
carlopecoraro2
★ 2.6k
0
votes
1
reply
147
views
BSQR in GATK without known variants
GATK
updated 13 hours ago by
Istvan Albert
101k • written 1 day ago by
fuwamozu
• 0
1
vote
5
replies
258
views
Can germline callers detect somatic variants? (RNAseq, cancer, no matched normal)
germline
somatic
RNA-seq
mutect2
deepvariant
updated 12 hours ago by
Istvan Albert
101k • written 1 day ago by
don
• 0
0
votes
0
replies
53
views
How to Reconstruct and Visualize Mitochondrial Primary Transcripts Using RNA-Seq Data?
RNA-Seq
mitochondria
transcriptomics
minimap2
updated 13 hours ago by
GenoMax
147k • written 14 hours ago by
hashim.rana11
▴ 40
1
vote
7
replies
192
views
metaspades error
metaspades
50 minutes ago by
pranjalarun10
• 0
0
votes
1
reply
111
views
Multiple entries in a some columns on FeatureCounts output
FeatureCounts
updated 17 hours ago by
biofalconch
★ 1.3k • written 1 day ago by
myoui3122010
▴ 20
1
vote
9
replies
273
views
How do I integrate public annotated data onto my data set?
SelectIntegrationFeatures
IntegrateData
Seurat
tabula-muris
updated 13 hours ago by
Bastien Hervé
5.8k • written 21 hours ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
110
views
Problem in count Matrix from Featurecount
countMatrix
Featurecount
BAM
updated 17 hours ago by
GenoMax
147k • written 21 hours ago by
daffodil
▴ 10
0
votes
2
replies
145
views
Integrating TCGA tumor RNAseq data with normal tissue samples from other sources
rna-seq
prps
dge
tcga
ruv-iii
21 hours ago by
CielDV
• 0
1
vote
5
replies
1.0k
views
Subset Seurat Object based on metadata
Seurat
updated 1 day ago by
aurelien.pelissier.38
• 0 • written 5 months ago by
Bine
▴ 90
0
votes
2
replies
141
views
how to get genomic location of transcript positions
genomic-location
m6Anet
updated 1 day ago by
GenoMax
147k • written 1 day ago by
baibhu1234
• 0
0
votes
0
replies
94
views
News:
Phylogenomics course - online Dec 2-6
Bayesian-Analyses
Phylogenomics
Genomics-data
updated 1 day ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.6k
0
votes
6
replies
229
views
WES and GBAP1
wes
homology
gba
ngs
13 hours ago by
Joel Wallenius
▴ 210
0
votes
0
replies
91
views
Minimum number of replicates when doing scRNA-seq using cell-lines?
design
10x
single-cell
1 day ago by
txema.heredia
▴ 190
1
vote
1
reply
146
views
DESeq2: error in checkFullRank(modelMatrix)
DESeqDataSet
design
DESeq2
RNA-Seq
updated 1 day ago by
cfos4698
★ 1.1k • written 1 day ago by
tilia
• 0
0
votes
0
replies
85
views
Is It Possible to Calculate Microsatellite Instability (MSI) Directly from MAF Files or TCGA Data?
instability
maf
Microsatellite
MSI
1 day ago by
Jaber
▴ 30
1
vote
3
replies
183
views
IGV: first bases of each chromosomes missing when loading genome file
IGV
updated 13 hours ago by
Istvan Albert
101k • written 1 day ago by
Pierre
• 0
6
votes
4
replies
243
views
Workstation RAM speed vs capacity
NGS
workstation
AI
updated 23 hours ago by
LChart
4.5k • written 1 day ago by
r.d.jongh
▴ 20
3
votes
6
replies
298
views
Why there are 40 chromosomes of Gallus gallus in NCBI and in the in karyotype studies there is only evidence of 39 chromosome
genome-assembly
updated 1 day ago by
Ram
44k • written 1 day ago by
BenAawf
▴ 10
1
vote
2
replies
141
views
somatic copy number calling with ONT long-reads
ONT
somatic
cancer
CNV
nanopore
1 day ago by
eebloom
▴ 90
4
votes
3
replies
284
views
Biostatistics
ANOVA
Post
Biostatistics
Hoc
updated 1 day ago by
Gordon Smyth
★ 7.6k • written 2 days ago by
RCMC
• 0
0
votes
0
replies
95
views
Input for Powermarker
Powermarker
SNP
updated 1 day ago by
GenoMax
147k • written 1 day ago by
Smilesky
• 0
0
votes
0
replies
91
views
TCRdist3
TCRdist3
TCR
VDJ
1 day ago by
jl_oxforduni
• 0
0
votes
0
replies
100
views
No gene and PAV has overlap warning while constructing pangenome
pangenome
1 day ago by
analyst
▴ 50
0
votes
1
reply
191
views
How to compare and complement the missing gene and feature in gff3 file base on available gff3 reference ?
gff3
IRGSP1.0
MAKER
updated 1 day ago by
lieven.sterck
15k • written 2 days ago by
Sony
▴ 10
0
votes
0
replies
100
views
Calculating TMB for TCGA data
mutations
maftools
TMB
1 day ago by
Jaber
▴ 30
0
votes
1
reply
144
views
how do you open a networks file which gets from the Cytoscape by using python package networkx?
python
bioinformatics
Cytoscape
networkx
updated 1 day ago by
Wayne
★ 2.1k • written 2 days ago by
雨
▴ 20
1
vote
5
replies
1.7k
views
6 follow
Can I combine the GBS data with Whole Genome Resequencing for GWAS analysis
sequencing
snp
updated 1 day ago by
behnam
▴ 10 • written 6.0 years ago by
gengyang12138
▴ 20
2
votes
4
replies
252
views
Need to remove duplicates from GBS data?
GBS
Samblaster
Duplicates
1 day ago by
MMW
• 0
0
votes
1
reply
275
views
fragment size estimation during vg mpmap and rpvg
vg
updated 2 days ago by
Jordan M Eizenga
▴ 640 • written 6 weeks ago by
Juhyun
• 0
0
votes
0
replies
131
views
Junction Saturation for AS analysis
ONT
splice-junctions
updated 1 day ago by
Ram
44k • written 2 days ago by
coolmattmonkey
• 0
0
votes
1
reply
147
views
MISO Sorted BAM file header mismatch
bam
miso
sam
minimap2
updated 11 hours ago by
Istvan Albert
101k • written 2 days ago by
bimeva5703
• 0
0
votes
10
replies
688
views
7 follow
The BUSCO assessment of the MAKER annotation results shows a low completeness
BUSCO
MAKER
1 hour ago by
mut
• 0
0
votes
1
reply
159
views
Aptamer design
Aptamer
updated 2 days ago by
Matthias Zepper
5.0k • written 2 days ago by
MUHAMMAD SHAFIQ
• 0
2
votes
1
reply
398
views
Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
DEGseq
DESeq2
EdgeR
RNAseq
updated 2 days ago by
GenoMax
147k • written 2 days ago by
Jonathan
• 0
1
vote
0
replies
127
views
I want to run fisher's exact test on my haplotype data for multiple genes.
Haplotype
2 days ago by
vinita14ramtekey
▴ 10
0
votes
1
reply
155
views
Merging multiple runs of the same samples
metaspades
fastq
Megahit
shotgun
metagenomics
sequencing
updated 2 days ago by
GenoMax
147k • written 2 days ago by
bioinformaticssrm2011
▴ 90
119,597 results • Page
1 of 2392
Recent Votes
Answer: Getting gnomAD allele frequencies for checking against populations
Answer: [RNASeq] Excluding samples that cluster differently in PCA plot
Answer: Using reference genome for GSEA for different strains of the same bacterial spec
Answer: How to include the lane index in STARsolo count matrix barcodes.tsv?
Comment: DESeq2: error in checkFullRank(modelMatrix)
Comment: Merge braker.gtf and SQANT3.gff3 file
Getting gnomAD allele frequencies for checking against populations
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Comment: metaspades error
by
pranjalarun10
• 0
Trimming was done independently for both R1 and R2 files i.e., with trimming option of trimming base pair less than 35 bp and Q less than 30
Comment: The BUSCO assessment of the MAKER annotation results shows a low completeness
by
mut
• 0
I used the BUSCO embryophyta_odb10 database and Maker v3.01.03
Comment: making estimated proteome from genome
by
GenoMax
147k
> The only thing that I can think of is to use prodigal on each of the 2099 individual contigs, and then combine them later. If it works t…
Comment: Demultiplexing inDrop dataset
by
jade
• 0
Hello, The page "https://iccb.med.harvard.edu/files/iccb/files/sequencing_indrops_libraries_02_28_18.pdf" cannot be found. Could you please…
Comment: Combine GBS and WGS data for variant calling in GWAS analysis
by
behnam
▴ 10
Thanks for your comment. I think in your comment, you mean we should analyze the parents and population separately, then combine the cover…
Comment: How to include the lane index in STARsolo count matrix barcodes.tsv?
by
swbarnes2
14k
Why do you want to do this? Does Illumina even make instruments anymore where you can have one sample in one lane, and a different sample …
Comment: Seurat - unordered cells
by
solo.albif
• 0
I started my analysis with a single Seurat object and used `SplitObject(object, split.by = "ident")` to split by Patient ID. The problem wi…
Comment: How to include the lane index in STARsolo count matrix barcodes.tsv?
by
mk
▴ 300
thanks, so how do i make starsolo report the NNNNNNNN-i index of the gem well for barcode NNNNNNNN?
Answer: How to include the lane index in STARsolo count matrix barcodes.tsv?
by
swbarnes2
14k
If you combine two samples together, the -1 and -2 at the end of cell barcodes will matter, so you know what cells came from what samples, …
Answer: miloR - object 'as.SimpleList' of mode 'function' was not found when running cal
by
michael.morgan
• 0
FYI - this didn't get tagged as miloR, so it didn't come up on my radar. First thing is, hopefully you aren't still having a problem. Se…
Comment: How to Identify Strain-Specific HPV and EBV Integration Sites in Human Whole Gen
by
GenoMax
147k
Similar analyses have been published before which should help you get started . https://onlinelibrary.wiley.com/doi/pdf/10.1002/ctm2.971<b…
Comment: How to Identify Strain-Specific HPV and EBV Integration Sites in Human Whole Gen
by
GenoMax
147k
> any tips on where to find reliable reference genomes for HPV and EBV would be helpful. Search here: https://www.ncbi.nlm.nih.gov/dataset…
Comment: Can I combine variants called using T2T-CHM13 with GRCh38?
by
Jeremy Leipzig
22k
i would be alarmed if new stuff was showing up in exomes. it is an interesting idea though.
Answer: Can I combine variants called using T2T-CHM13 with GRCh38?
by
Istvan Albert
101k
I would keep the two variants separate. Each variant call process may have problems, though those called for T2T would have fewer errors ar…
Comment: MISO Sorted BAM file header mismatch
by
Istvan Albert
101k
the error message seems very clear about the problem: Your chromosome names do not match. You show a lot of code above, but what are the…
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