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51 results • Page
1 of 2
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0
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0
replies
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Genome Visualization Tools
bacterial
genomes
genome
just now by
dlera.lozano
• 0
0
votes
1
reply
12
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
Strandness
RNASeq
updated 3 minutes ago by
Trivas
★ 1.7k • written 6 minutes ago by
Prawesh
• 0
0
votes
1
reply
24
views
Using ggplotly in R
ggplot
ggplotly
updated 1 minute ago by
jared.andrews07
★ 16k • written 54 minutes ago by
jen
▴ 10
0
votes
1
reply
36
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 43 minutes ago by
GenoMax
142k • written 1 hour ago by
bioinfo
▴ 150
0
votes
3
replies
123
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 1 hour ago by
noodle
▴ 580 • written 5 hours ago by
doramora
▴ 10
0
votes
1
reply
51
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 2 hours ago by
LauferVA
4.2k • written 3 hours ago by
graeme.thorn
▴ 100
0
votes
1
reply
56
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
melissa.joubert
• 0
0
votes
0
replies
40
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
3 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
135
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
5 hours ago by
J.
▴ 40
0
votes
0
replies
47
views
Is there a real ground truth for CNV data?
CNV
6 hours ago by
jennyp0706
• 0
0
votes
3
replies
149
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 6 hours ago by
GenoMax
142k • written 20 hours ago by
RNAseqer
▴ 270
1
vote
1
reply
81
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 1 hour ago by
Ram
43k • written 6 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
42
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 6 hours ago by
GenoMax
142k • written 7 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 8 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
6
replies
244
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
3 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
146
views
How to access GWAVA software of data
GWAVA
updated 7 hours ago by
GenoMax
142k • written 10 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
117
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 12 hours ago by
ATpoint
82k • written 19 hours ago by
Chen
• 0
0
votes
1
reply
108
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 11 hours ago by
ATpoint
82k • written 16 hours ago by
Pegasus
▴ 100
0
votes
1
reply
90
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 12 hours ago by
ATpoint
82k • written 16 hours ago by
Emily
▴ 20
1
vote
1
reply
133
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 12 hours ago by
zx8754
11k • written 19 hours ago by
ohtang7
▴ 40
0
votes
0
replies
57
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
14 hours ago by
Spring
• 0
0
votes
2
replies
124
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
11 hours ago by
IdaHao0921
• 0
0
votes
3
replies
294
views
Snakemake wrapper issue
fastqc
snakemake
updated 15 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
80
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
16 hours ago by
Holly
• 0
2
votes
5
replies
208
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 16 hours ago by
Philipp Bayer
8.5k • written 20 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 17 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
100
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
20 hours ago by
Arton
• 0
2
votes
4
replies
151
views
Help with IGV abbreviation
Genome
browser
19 hours ago by
GeneC
• 0
0
votes
1
reply
121
views
How to process Bulk WES data?
WES
WGS
updated 22 hours ago by
GenoMax
142k • written 23 hours ago by
wyuan37
• 0
0
votes
1
reply
122
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 21 hours ago by
GenoMax
142k • written 23 hours ago by
cedric.blais
• 0
0
votes
1
reply
110
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 22 hours ago by
Ram
43k • written 1 day ago by
eking28
• 0
1
vote
2
replies
224
views
How to interpret infinite odds ratio?
statistics
9 hours ago by
Lukas
• 0
0
votes
1
reply
109
views
Splitting Seurat object by sample layers
seurat
updated 22 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
4
replies
205
views
Galaxy StringTie error
stringtie
galaxy
9 hours ago by
trkfs
• 0
1
vote
3
replies
214
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
12 hours ago by
Vijith
▴ 30
0
votes
3
replies
155
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
yau
• 0
3
votes
2
replies
244
views
imputation through beagle
panel
beagle
reference
imputation
12 hours ago by
analyst
▴ 50
2
votes
4
replies
276
views
BWA alignment
Samtools
bam
updated 13 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
0
votes
1
reply
229
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 22 hours ago by
Ram
43k • written 5 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 9 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
3
votes
3
replies
315
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 20 hours ago by
Mathew
▴ 140 • written 3 days ago by
Christopher
• 0
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 22 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
1
vote
4
replies
325
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 22 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
0
votes
1
reply
140
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 22 hours ago by
Ram
43k • written 7 days ago by
David
• 0
4
votes
7
replies
380
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
19 hours ago by
Chen
• 0
3
votes
3
replies
254
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 22 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 22 hours ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
177
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
16 hours ago by
Emily
▴ 20
2
votes
3
replies
257
views
Finding variants within a subset of a BAM file
variant
calling
4 hours ago by
ramiro.barrantes
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 20 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
51 results • Page
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Recent Votes
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
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
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Recent Replies
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.7k
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?
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?
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