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45 results • Page
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News:
Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
single
RNA-Seq
scRNA-Seq
cell
workshop
24 minutes ago by
David Langenberger
10k
0
votes
3
replies
122
views
Importance of Data Structures for Bioinformatics?
structures
data
Industry
Bioinformatic
updated 28 minutes ago by
xiaoguang
▴ 120 • written 7 hours ago by
S
• 0
0
votes
2
replies
92
views
How to find positions with higher depth relative to their surroundings
depth
python
samtools
updated 1 hour ago by
xiaoguang
▴ 120 • written 8 hours ago by
hyperdx1
• 0
0
votes
0
replies
30
views
News:
Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sars-cov-2
spikePprotein
computationalApproach
escapeMutations
sequenceAanalysis
3 hours ago by
Prem
• 0
0
votes
2
replies
122
views
How to retrieve LoF and missense variants in WES data?
bcftools
variants
plink
SNPs
updated 3 hours ago by
luffy
▴ 30 • written 20 hours ago by
_quantum_girl_
▴ 10
0
votes
1
reply
121
views
Recommended order of operations for identifying the genomic location and copy-number of an insert with a known sequence from WGS Nanopore fastq files
Sequencing
WGS
Nanopore
Long-Read
5 hours ago by
dk0319
▴ 70
3
votes
1
reply
82
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 11 hours ago by
Ram
40k • written 12 hours ago by
a615ebfb
▴ 30
1
vote
0
replies
77
views
Herald:
The Biostar Herald for Wednesday, September 20, 2023
herald
13 hours ago by
Biostar
2.0k
0
votes
0
replies
70
views
Chromosome bias on RNA-Seq differential gene expression analysis
bias
rna-seq
chromosome
13 hours ago by
blz
▴ 10
1
vote
4
replies
168
views
I need to retrieve a set of protein and mRNA sequences
Protein
mRNA
sequences
updated 12 hours ago by
Ram
40k • written 14 hours ago by
george
• 0
0
votes
1
reply
93
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
entrez
esearch
biopython
efetch
epost
updated 13 hours ago by
GenoMax
134k • written 13 hours ago by
Salem
• 0
1
vote
2
replies
128
views
GSEA Result Visualization in R
r
enrichplot
gsea
visualization
enrichResult
13 hours ago by
Cortney
• 0
1
vote
2
replies
161
views
How to seperate proteins on the same chain?
pdb
protein
updated 15 hours ago by
Jeremy
▴ 840 • written 1 day ago by
Zayyan
▴ 10
0
votes
2
replies
132
views
how to evaluate SNPs that are regulating same gene expression across multiple tissues
snp
GTEx
updated 15 hours ago by
LChart
3.3k • written 17 hours ago by
rheab1230
▴ 140
1
vote
6
replies
200
views
STAR index not working
STAR
RNA-Seq
updated 14 hours ago by
Ram
40k • written 16 hours ago by
camillab.
▴ 130
2
votes
2
replies
164
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
updated 16 hours ago by
GenoMax
134k • written 1 day ago by
edoardoscali.93
• 0
1
vote
2
replies
283
views
How to display all top markers in the heatmap by DoHeatmap (Seurat) when there are duplicates of top marker genes for several cell clusters
DoHeatmap
Seurat
11 hours ago by
alwayshope
▴ 30
0
votes
2
replies
117
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 9 hours ago by
swbarnes2
13k • written 17 hours ago by
Mo
• 0
1
vote
3
replies
168
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 15 hours ago by
Ram
40k • written 17 hours ago by
txema.heredia
▴ 80
0
votes
1
reply
83
views
Prank checkpoint and restore?
prank
alignment
updated 17 hours ago by
Ram
40k • written 17 hours ago by
Pit
• 0
0
votes
0
replies
208
views
Job:
Research Scientist 5 – Bioinformatics and Computer Biology, Center for Dementia Research (CDR), Nathan Kline Institute for Psychiatric Research
Neuroscience
Biostatistics
updated 18 hours ago by
Ram
40k • written 18 hours ago by
cdrinfo
• 0
0
votes
1
reply
113
views
gffread outputs empty gtf file
gff
gffread
gtf
updated 19 hours ago by
inedraylig
▴ 20 • written 22 hours ago by
sumitra.20
• 0
0
votes
10
replies
299
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
16 hours ago by
Y
• 0
3
votes
7
replies
347
views
Elusive syntax error in Snakefile
snakemake
updated 18 hours ago by
Ram
40k • written 1 day ago by
Giuseppe Giovanni
▴ 20
1
vote
3
replies
156
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 18 hours ago by
GenoMax
134k • written 20 hours ago by
anika.john
• 0
8
votes
10
replies
575
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype
imputation
gwas
updated 6 hours ago by
LauferVA
3.7k • written 1 day ago by
Amy
▴ 20
2
votes
7
replies
244
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
updated 19 hours ago by
i.sudbery
17k • written 21 hours ago by
langziv
▴ 50
2
votes
2
replies
138
views
Kraken2 recovering only classified reads
Kraken2
taxonomy
classification
20 hours ago by
SushiRoll
▴ 110
0
votes
1
reply
111
views
Identifying common DEGs among multiple datasets
R
DEG
updated 14 hours ago by
bk11
★ 1.2k • written 22 hours ago by
Shma
• 0
0
votes
0
replies
68
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 18 hours ago by
Ram
40k • written 22 hours ago by
Mark
• 0
0
votes
0
replies
74
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
updated 18 hours ago by
Ram
40k • written 23 hours ago by
Thomas
• 0
2
votes
4
replies
224
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 18 hours ago by
Ram
40k • written 1 day ago by
P
• 0
6
votes
6
replies
305
views
Adding a control sample to bulk RNA-seq
RNA-seq
3 hours ago by
Chris
▴ 180
18
votes
14
replies
630
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 14 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
vincenthus
▴ 60
0
votes
2
replies
179
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
17 hours ago by
JLee
• 0
2
votes
3
replies
204
views
Is there an easy to modify the subplot titles in DimPlot (Seurat)?
scRNA-seq
patchwork
DimPlot
Seurat
updated 23 hours ago by
Nicolas Rosewick
10k • written 1 day ago by
alwayshope
▴ 30
0
votes
4
replies
248
views
manhattan plot with vcf information
R
manhattan
vcf
5 hours ago by
sooni
▴ 10
3
votes
2
replies
388
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 19 hours ago by
yhdist
▴ 70 • written 3 days ago by
Cookin
• 0
0
votes
11
replies
649
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
15 hours ago by
evmae
• 0
0
votes
3
replies
1.2k
views
how to calculate BAF and LRR from VCF or BCF files?
SNP
BAF
LRR
Variation
1 hour ago by
xiaoguang
▴ 120
3
votes
2
replies
462
views
Conflict between MAFFT and new PRANK installation
multiple-sequence-alignment
bash
prank
mafft
phylogenetics
updated 17 hours ago by
Ram
40k • written 19 months ago by
noramarie
• 0
2
votes
7
replies
4.0k
views
GERP++ (gerpcol) error on a test data
GERP
updated 2 hours ago by
Diana
• 0 • written 7.1 years ago by
kirill1984
▴ 10
1
vote
6
replies
3.2k
views
Extracting sequence, not reads, by position from bam
sequence
updated 22 hours ago by
manu
• 0 • written 5.0 years ago by
geneware
▴ 10
0
votes
3
replies
2.0k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 23 hours ago by
aishwarya
• 0 • written 5.2 years ago by
blooming.daisy333
▴ 110
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 14 hours ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
45 results • Page
1 of 1
Recent Votes
C: bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the si
What is the difference between norm --multiallelics -any versus --atomize?
Answer: What is the difference between norm --multiallelics -any versus --atomize?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
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Popular Question
to
zx8754
11k
Popular Question
to
xiaoguang
▴ 120
Popular Question
to
luffy
▴ 30
Teacher
to
swbarnes2
13k
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blz
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Ram
40k
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Recent Replies
Answer: Importance of Data Structures for Bioinformatics?
by
xiaoguang
▴ 120
Bioinformatics is a cross-disciplinary research subject and learning anything is a plus for future participation in related jobs. But right…
Answer: How to find positions with higher depth relative to their surroundings
by
xiaoguang
▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files?
by
xiaoguang
▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data
by
Diana
• 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings
by
d-cameron
★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data?
by
luffy
▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
Answer: Importance of Data Structures for Bioinformatics?
by
d-cameron
★ 2.9k
> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
Answer: Recommended order of operations for identifying the genomic location and copy-nu
by
dk0319
▴ 70
Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
Comment: manhattan plot with vcf information
by
sooni
▴ 10
I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
Comment: Importance of Data Structures for Bioinformatics?
by
dsull
★ 4.6k
If you don't want to hurt your GPA, why not just take the course pass/fail or, if that's not an option, simply audit it? I doubt anyone wi…
Comment: How to DESeq2 using miRNA data obtained using TCGAbiolinks
by
swbarnes2
13k
miRNAs are rather small, and your typical RNASeq library prep will remove small sequences. Are you sure that the data you are trying to ge…
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset
by
LauferVA
3.7k
even these measures will very often not fix the problem in the context of a problem of a problem of perfect separation such as OP describes.
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset
by
LauferVA
3.7k
Hi Amy, I understand, this is why I said, > "The degree to which this is possible depends on the relative content > of each study - e.g. …
Answer: What is the difference between norm --multiallelics -any versus --atomize?
by
Ram
40k
I don't think atomization compares to norm with respect to multiallelic sites. You can see an example of atomatization on a multi-allelic s…
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