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686 results • Page
2 of 14
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
202
views
constructing pangenome through psvcp
psvcp
pangenome
2 days ago by
analyst
▴ 50
0
votes
3
replies
265
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 10 hours ago by
nd48
▴ 20 • written 3 days ago by
Umer
▴ 50
0
votes
4
replies
348
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 2 days ago by
txema.heredia
▴ 130 • written 3 days ago by
Ngrin
• 0
4
votes
9
replies
491
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
3 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
251
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
0
votes
0
replies
134
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
3 days ago by
Varsha
• 0
0
votes
1
reply
417
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 3 days ago by
GenoMax
142k • written 3 days ago by
huxiangyulove
• 0
0
votes
0
replies
151
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
3 days ago by
O.rka
▴ 720
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 3 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
340
views
Merge clusters in Seurat UMAP
seurat
umap
3 days ago by
kilcdincer
▴ 10
0
votes
0
replies
158
views
Use of ichor CNA
Dog
CNA
genome
3 days ago by
sainavyav22
• 0
2
votes
2
replies
275
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
txema.heredia
▴ 130
1
vote
0
replies
167
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 3 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
356
views
Details on salmon index
Salmon
updated 3 days ago by
Rob
6.6k • written 4 days ago by
Lorenzo
• 0
0
votes
0
replies
160
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
4 days ago by
Jsarria.EEAD
• 0
0
votes
1
reply
213
views
How can I calculate the OS of each patient?
overall-survival
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Pedro
• 0
1
vote
1
reply
218
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
m90
▴ 30
0
votes
0
replies
153
views
cat-bgen fail
bgenix
updated 4 days ago by
Ram
43k • written 4 days ago by
lambard
• 0
3
votes
4
replies
341
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 3 days ago by
Jeremy Leipzig
22k • written 4 days ago by
Ali
• 0
3
votes
3
replies
252
views
getting exon coordinates
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Xbox_27
• 0
0
votes
4
replies
333
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 3 days ago by
Tony
• 0 • written 4 days ago by
vk
▴ 10
1
vote
5
replies
324
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 3 days ago by
Ram
43k • written 4 days ago by
manuelmourato25
• 0
3
votes
4
replies
415
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Pierre Lindenbaum
161k
2
votes
11
replies
736
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
3 days ago by
egascon
• 0
1
vote
1
reply
202
views
API kegg - IndexError: list index out of range
kegg
API
updated 3 days ago by
Nyksubuz
▴ 20 • written 4 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
146
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
4 days ago by
Novogene
▴ 420
0
votes
0
replies
143
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
4 days ago by
ebertomeup
• 0
0
votes
3
replies
283
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
1
vote
3
replies
288
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 5 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
594
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 4 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
147
views
select set of intervals that cover a genomic region
GRanges
bed
4 days ago by
ntsopoul
▴ 60
1
vote
1
reply
197
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 3 days ago by
Ram
43k • written 4 days ago by
dwpeng
▴ 10
0
votes
2
replies
214
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
14 hours ago by
Luqman
• 0
2
votes
3
replies
258
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
4
replies
287
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
2 days ago by
mavy
▴ 10
1
vote
1
reply
250
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
4 days ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 4 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
178
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 4 days ago by
Michael
54k • written 4 days ago by
mgranada3
▴ 30
0
votes
1
reply
157
views
Add line under stat test
stats
R
updated 3 days ago by
Nyksubuz
▴ 20 • written 4 days ago by
Ghada
• 0
1
vote
5
replies
810
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
115
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Rodolfo Adrián
• 0
1
vote
3
replies
210
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
shpak.max
▴ 50
2
votes
4
replies
277
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 days ago by
yura.grabovska
▴ 90 • written 5 days ago by
ev97
▴ 20
1
vote
16
replies
756
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 2 days ago by
GenoMax
142k • written 5 days ago by
hophuquy0944
• 0
0
votes
4
replies
248
views
Sequencing Depth (Read Depth) Calculations
depth
4 days ago by
LucisTheFather
• 0
0
votes
1
reply
141
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
5 days ago by
asalimih
▴ 60
0
votes
0
replies
112
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
5 days ago by
jway
• 0
2
votes
2
replies
193
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 4 days ago by
Ram
43k • written 5 days ago by
jsmith120f
• 0
2
votes
2
replies
206
views
genome finishing
finishing
genome
updated 5 days ago by
nd48
▴ 20 • written 5 days ago by
trezini
• 0
1
vote
5
replies
231
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
biology_inform
▴ 50
686 results • Page
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Answer: Generating Group/Cluster Lists from fastq files
The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
C: Cleaning RNA-Seq data from rRNA
Answer: How to find identical sequences in genome fasta file (by Python or any possible
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Answer: Error in using BioSampleParser tool: subscript out of bounds
by
Mohamed Samir
▴ 20
Dear marco, We need to ask ourselves why it is not working for all bioprojects ? I have looked into this, and observed that as long as the…
Comment: Why most genes have high padj values
by
Ram
43k
You ***want*** ~3000 DE genes?<a href="" title="Text added because biostars parser needs it"></a>
Answer: Generating Group/Cluster Lists from fastq files
by
GenoMax
142k
> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
Comment: Super ehancers
by
jared.andrews07
★ 16k
Based on the [source code](https://bitbucket.org/young_computation/rose/src/feb35cb1d9556a76f8ac1f51521539bb30651343/ROSE_utils.py?at=maste…
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
Ram
43k
They're not addressing the actual question, just saying something tangentially related. It looks like their understanding of both consensus…
Comment: Super ehancers
by
Oburah
• 0
Hello, i encountered this problem when running ROSE, Do anyone know how to solve it? python2.7 ROSE_main.py -g HG38 -i /home/hesborn/…
Answer: How to generate an Upset plot in R to plot the shared variants between cell free
by
zx8754
11k
Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array
by
fu_entomology
▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
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