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674 results • Page
3 of 14
Sort: Rank
Rank
Views
Votes
Replies
4
votes
1
reply
207
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
5 days ago by
J.
▴ 40
0
votes
0
replies
112
views
Is there a real ground truth for CNV data?
CNV
5 days ago by
jennyp0706
• 0
0
votes
3
replies
217
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 5 days ago by
GenoMax
142k • written 5 days ago by
RNAseqer
▴ 270
1
vote
1
reply
148
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 5 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
8
replies
456
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 day ago by
Alex Reynolds
35k • written 5 days ago by
ntsopoul
▴ 60
0
votes
3
replies
209
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by
GenoMax
142k • written 5 days ago by
nonaddldy
▴ 10
0
votes
2
replies
229
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
3 days ago by
Chen
• 0
1
vote
1
reply
176
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Pegasus
▴ 100
0
votes
1
reply
133
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 4 days ago by
Ram
43k • written 5 days ago by
Emily
▴ 20
1
vote
3
replies
279
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 2 days ago by
GenoMax
142k • written 5 days ago by
ohtang7
▴ 40
0
votes
0
replies
95
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
5 days ago by
Spring
• 0
0
votes
2
replies
186
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
0
votes
3
replies
355
views
Snakemake wrapper issue
fastqc
snakemake
updated 5 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
280
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 5 days ago by
Philipp Bayer
8.5k • written 5 days ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 4 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
231
views
Help with IGV abbreviation
igv
updated 4 days ago by
Ram
43k • written 5 days ago by
GeneC
• 0
0
votes
1
reply
162
views
How to process Bulk WES data?
WES
WGS
updated 5 days ago by
GenoMax
142k • written 5 days ago by
wyuan37
• 0
0
votes
1
reply
162
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 5 days ago by
GenoMax
142k • written 5 days ago by
cedric.blais
• 0
0
votes
2
replies
438
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
5 days ago by
David Langenberger
11k
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 5 days ago by
Ram
43k • written 5 days ago by
eking28
• 0
2
votes
5
replies
499
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 4 days ago by
Ram
43k • written 10 days ago by
Prawesh
• 0
1
vote
3
replies
446
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
5 days ago by
kalavattam
▴ 190
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
5 days ago by
Lukas
• 0
1
vote
2
replies
185
views
Duplicated sequence samtools
bowtie2
samtools
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Moinuddin
• 0
0
votes
0
replies
105
views
reference-free assembly error assessment tools
assembly
5 days ago by
lagartija
▴ 160
2
votes
4
replies
307
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
4 days ago by
Esraa
• 0
2
votes
0
replies
144
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
5 days ago by
Biostar
2.8k
0
votes
1
reply
144
views
Splitting Seurat object by sample layers
seurat
updated 5 days ago by
Ram
43k • written 6 days ago by
kilcdincer
▴ 10
0
votes
4
replies
263
views
Galaxy StringTie error
stringtie
galaxy
5 days ago by
trkfs
• 0
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
6 days ago by
atariw
▴ 10
0
votes
1
reply
159
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 6 days ago by
GenoMax
142k • written 6 days ago by
octpus616
▴ 100
1
vote
4
replies
352
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 6 days ago by
Vijith
▴ 30
0
votes
1
reply
165
views
consensus sequence calling
consensus
updated 6 days ago by
bk11
★ 2.5k • written 6 days ago by
Ghada
• 0
0
votes
3
replies
195
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 5 days ago by
Ram
43k • written 6 days ago by
yau
• 0
3
votes
2
replies
287
views
imputation through beagle
panel
beagle
reference
imputation
5 days ago by
analyst
▴ 50
0
votes
0
replies
89
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
6 days ago by
JACKY
▴ 140
0
votes
1
reply
542
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 6 days ago by
aw7
▴ 300 • written 29 days ago by
abhishekghadge
• 0
3
votes
1
reply
218
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 6 days ago by
aw7
▴ 300 • written 10 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
6 days ago by
gernophil
▴ 80
1
vote
0
replies
99
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
6 days ago by
tomas4482
▴ 400
2
votes
6
replies
404
views
BWA alignment
Samtools
bam
updated 4 days ago by
a.alnawfal.1992
▴ 260 • written 6 days ago by
Vahid
• 0
3
votes
2
replies
199
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 6 days ago by
ATpoint
82k • written 6 days ago by
jennyp0706
• 0
0
votes
1
reply
160
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 6 days ago by
Philipp Bayer
8.5k • written 6 days ago by
samRayne
• 0
0
votes
1
reply
247
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 5 days ago by
Ram
43k • written 9 days ago by
Nikki
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 5 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
198
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 6 days ago by
chrchang523
10k • written 11 days ago by
analyst
▴ 50
0
votes
0
replies
112
views
lncRNA
tcga
lncrna
6 days ago by
jain72744
▴ 10
0
votes
1
reply
244
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
jain72744
▴ 10
2
votes
5
replies
597
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 6 days ago by
arctic
▴ 40 • written 16 days ago by
M.
▴ 30
674 results • Page
3 of 14
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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carlopecoraro2
★ 2.5k
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scideas
▴ 30
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Recent Replies
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
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★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
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21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
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