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891 results • Page
1 of 18
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0
votes
0
replies
12
views
Post-imputation QC for input into GWAS analyses
gwas
prs
50 minutes ago by
graeme.thorn
▴ 100
0
votes
1
reply
21
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 18 minutes ago by
GenoMax
142k • written 1 hour ago by
melissa.joubert
• 0
0
votes
0
replies
17
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 hour ago by
ramiro.barrantes
• 0
0
votes
2
replies
71
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA
RNAseq
updated 1 hour ago by
ntsopoul
▴ 60 • written 2 hours ago by
doramora
▴ 10
4
votes
1
reply
113
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
3 hours ago by
J.
▴ 40
0
votes
0
replies
35
views
Is there a real ground truth for CNV data?
CNV
3 hours ago by
jennyp0706
• 0
0
votes
3
replies
124
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 3 hours ago by
GenoMax
142k • written 17 hours ago by
RNAseqer
▴ 270
0
votes
1
reply
56
views
sci-RNA-seq
sci-RNA-seq
clusters
combinatorial
single
2 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
32
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 6 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
6
replies
184
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
1 hour ago by
ntsopoul
▴ 60
0
votes
3
replies
121
views
How to access GWAVA software of data
GWAVA
updated 4 hours ago by
GenoMax
142k • written 7 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
112
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 10 hours ago by
ATpoint
82k • written 16 hours ago by
Chen
• 0
0
votes
1
reply
101
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 9 hours ago by
ATpoint
82k • written 14 hours ago by
Pegasus
▴ 100
0
votes
1
reply
80
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 10 hours ago by
ATpoint
82k • written 13 hours ago by
Emily
▴ 20
1
vote
1
reply
122
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 10 hours ago by
zx8754
11k • written 17 hours ago by
ohtang7
▴ 40
0
votes
0
replies
52
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
11 hours ago by
Spring
• 0
0
votes
2
replies
113
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
8 hours ago by
IdaHao0921
• 0
0
votes
3
replies
284
views
Snakemake wrapper issue
fastqc
snakemake
updated 12 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
74
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
13 hours ago by
Holly
• 0
2
votes
5
replies
195
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 13 hours ago by
Philipp Bayer
8.5k • written 17 hours ago by
林明德
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 14 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
98
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
17 hours ago by
Arton
• 0
2
votes
4
replies
146
views
Help with IGV abbreviation
Genome
browser
16 hours ago by
GeneC
• 0
0
votes
1
reply
118
views
How to process Bulk WES data?
WES
WGS
updated 19 hours ago by
GenoMax
142k • written 20 hours ago by
wyuan37
• 0
0
votes
1
reply
117
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 18 hours ago by
GenoMax
142k • written 21 hours ago by
cedric.blais
• 0
0
votes
2
replies
388
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
21 hours ago by
David Langenberger
11k
0
votes
1
reply
107
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 19 hours ago by
Ram
43k • written 21 hours ago by
eking28
• 0
1
vote
4
replies
370
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 21 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
330
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
22 hours ago by
kalavattam
▴ 190
1
vote
2
replies
214
views
How to interpret infinite odds ratio?
statistics
7 hours ago by
Lukas
• 0
1
vote
2
replies
132
views
Duplicated sequence samtools
bowtie2
samtools
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
Moinuddin
• 0
0
votes
0
replies
76
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
1
vote
2
replies
169
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 1 day ago by
lagartija
▴ 160 • written 1 day ago by
Esraa
• 0
2
votes
0
replies
101
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
1 day ago by
Biostar
2.8k
0
votes
1
reply
107
views
Splitting Seurat object by sample layers
seurat
updated 19 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
4
replies
197
views
Galaxy StringTie error
stringtie
galaxy
7 hours ago by
trkfs
• 0
0
votes
0
replies
76
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
0
votes
1
reply
124
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 1 day ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
1
vote
3
replies
207
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
9 hours ago by
Vijith
▴ 30
0
votes
1
reply
129
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
152
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 19 hours ago by
Ram
43k • written 1 day ago by
yau
• 0
3
votes
2
replies
242
views
imputation through beagle
panel
beagle
reference
imputation
9 hours ago by
analyst
▴ 50
0
votes
0
replies
74
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
1
reply
453
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 1 day ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
191
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 1 day ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
90
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
1
vote
0
replies
86
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
2
votes
4
replies
270
views
BWA alignment
Samtools
bam
updated 10 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
3
votes
2
replies
167
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
891 results • Page
1 of 18
Recent Votes
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
Filtering multi-allelic sites in VCF files
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Recent Replies
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?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
• 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
by
ntsopoul
▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content
by
ATpoint
82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object
by
ATpoint
82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴ 40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
by
GenoMax
142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq
by
ATpoint
82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
Comment: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
Which species is this?
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
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