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88 results • Page
2 of 2
Sort: replies
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Votes
Replies
0
votes
1
reply
131
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
132
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
1
reply
81
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
melissa.joubert
• 0
1
vote
1
reply
94
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 5 hours ago by
Ram
43k • written 10 hours ago by
kilcdincer
▴ 10
0
votes
1
reply
89
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
bioinfo
▴ 150
0
votes
0
replies
149
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
5 days ago by
Aytaç
• 0
1
vote
0
replies
89
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
0
votes
0
replies
95
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
0
votes
0
replies
81
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
0
replies
156
views
supervised admixture
supervised
admixture
5 days ago by
RT
▴ 10
0
votes
0
replies
184
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
5 days ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
86
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
1
vote
0
replies
175
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
5 days ago by
eebloom
▴ 80
0
votes
0
replies
12
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
1 hour ago by
sansan_96
▴ 90
0
votes
0
replies
86
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
0
votes
0
replies
107
views
meffil.snp.concordance
meffil
methylation
snp_concordance
6 days ago by
kyj222637
• 0
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 1 day ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
5 days ago by
Javier
• 0
0
votes
0
replies
120
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
6 days ago by
Omics data mining
▴ 260
1
vote
0
replies
132
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
5 days ago by
Shae
▴ 10
0
votes
0
replies
7
views
Alphaphold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
11 minutes ago by
mbrav005
• 0
0
votes
0
replies
88
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
20 hours ago by
Holly
• 0
0
votes
0
replies
178
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
20 hours ago by
Emily
▴ 20
0
votes
0
replies
177
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
5 days ago by
Winter
• 0
0
votes
0
replies
64
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
18 hours ago by
Spring
• 0
0
votes
0
replies
115
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 5 days ago by
Ram
43k • written 5 days ago by
curious_butterfly
• 0
0
votes
0
replies
115
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
6 days ago by
asalimih
▴ 60
0
votes
0
replies
104
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 6 days ago by
Ram
43k • written 6 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
142
views
Chance for trained without experience
bio
updated 6 days ago by
ATpoint
82k • written 6 days ago by
shehab
• 0
0
votes
0
replies
52
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 11 hours ago by
GenoMax
142k • written 11 hours ago by
Bhavya
• 0
0
votes
0
replies
61
views
Is there a real ground truth for CNV data?
CNV
10 hours ago by
jennyp0706
• 0
0
votes
0
replies
62
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
7 hours ago by
ramiro.barrantes
• 0
0
votes
0
replies
103
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
2 days ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
158
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 4 days ago by
naomiboldon
• 0
0
votes
0
replies
99
views
lncRNA
tcga
lncrna
1 day ago by
jain72744
▴ 10
0
votes
0
replies
164
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 4 days ago by
zx8754
11k • written 5 days ago by
curious_butterfly
• 0
0
votes
0
replies
150
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
4 days ago by
Samantha
• 0
0
votes
0
replies
137
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
4 days ago by
singcell
• 0
88 results • Page
2 of 2
Recent Votes
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Comment: Genome Visualization Tools
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
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mbrav005
• 0
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Sofia
• 0
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jen
▴ 10
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nitinra
▴ 50
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43k
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bioinfo
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Recent Replies
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Comment: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
by
wyuan37
• 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses
by
LauferVA
4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
GenoMax
142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
does this work with a single .bed file?
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