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178 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
89
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
1 day ago by
Ayda Ecem
• 0
0
votes
3
replies
158
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 1 day ago by
Ram
44k • written 1 day ago by
pirku
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 1 day ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
555
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 1 day ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
88
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
1 day ago by
Yao
▴ 30
1
vote
1
reply
735
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
0
votes
0
replies
88
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
1 day ago by
dawnyipingzou
• 0
0
votes
4
replies
226
views
Where to find old version of GATK best practice
gatk
1 day ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
114
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 1 day ago by
Pierre Lindenbaum
162k • written 1 day ago by
Peter Chung
▴ 200
0
votes
0
replies
90
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 1 day ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
125
views
CreateSeuratObject taking very long
seurat
updated 1 day ago by
Nitin Narwade
★ 1.6k • written 1 day ago by
eae6d2e7
• 0
1
vote
2
replies
206
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
2 days ago by
ojaswinipandey
• 0
1
vote
4
replies
296
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 2 days ago by
Ram
44k • written 2 days ago by
Harshita
• 0
2
votes
4
replies
238
views
Filter Genome for Specific Sites
bedtools
updated 2 days ago by
Ram
44k • written 2 days ago by
Anita
• 0
0
votes
3
replies
250
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 2 days ago by
marco.barr
▴ 130 • written 2 days ago by
Mohamed Samir
▴ 20
1
vote
1
reply
126
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 2 days ago by
GenoMax
142k • written 2 days ago by
niruf
• 0
0
votes
0
replies
94
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 2 days ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
132
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
2 days ago by
Biostar
2.8k
3
votes
5
replies
435
views
Super ehancers
enhancers
updated 1 day ago by
jared.andrews07
★ 17k • written 20 days ago by
Oburah
• 0
0
votes
2
replies
181
views
vcf phasing
beagle
WhatsHap
phasing
17 hours ago by
safeassli
▴ 10
0
votes
2
replies
206
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
2 days ago by
sainavyav22
• 0
0
votes
1
reply
607
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 2 days ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
191
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 2 days ago by
Ram
44k • written 2 days ago by
Sony
▴ 10
0
votes
3
replies
200
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 2 days ago by
Ram
44k • written 2 days ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
93
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 2 days ago by
Ram
44k • written 2 days ago by
ev97
▴ 20
0
votes
1
reply
140
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 2 days ago by
marco.barr
▴ 130 • written 2 days ago by
sooni
▴ 20
0
votes
1
reply
106
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jinyi
• 0
0
votes
0
replies
83
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
2 days ago by
V_Vibes
• 0
0
votes
0
replies
157
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 2 days ago by
Ram
44k • written 2 days ago by
JorgeVallejo
▴ 20
0
votes
0
replies
101
views
transcriptome annotation
annotation
trinity
transcriptome
updated 2 days ago by
Ram
44k • written 2 days ago by
Asim Bin Arshad
• 0
0
votes
5
replies
227
views
Why most genes have high padj values
RNA-seq
DEG
updated 2 days ago by
Ram
44k • written 2 days ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 2 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
150
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 2 days ago by
zx8754
11k • written 2 days ago by
Ali
• 0
0
votes
4
replies
250
views
GO analysis: p-value range
GO
R
updated 2 days ago by
Matthias Zepper
4.6k • written 3 days ago by
sooni
▴ 20
1
vote
2
replies
231
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 1 day ago by
colindaven
6.4k • written 3 days ago by
Dr.
• 0
0
votes
3
replies
241
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 2 days ago by
GenoMax
142k • written 3 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
103
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
3 days ago by
Maryam
• 0
0
votes
4
replies
339
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
3 days ago by
Bibi
• 0
1
vote
2
replies
356
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 3 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
113
views
handling bio replicates for chromHMM
replicates
chromHMM
3 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
104
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
3 days ago by
DGTool
▴ 20
1
vote
1
reply
183
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 3 days ago by
ATpoint
82k • written 3 days ago by
rj.rezwan
• 0
0
votes
2
replies
326
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
3 days ago by
Ezequiel
• 0
2
votes
0
replies
190
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
3 days ago by
micah
▴ 30
0
votes
0
replies
120
views
problems in installing rDock
rDock
updated 2 days ago by
Ram
44k • written 3 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 3 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
729
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 3 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
384
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
139
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 4 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
Mohamed Samir
▴ 20
178 results • Page
2 of 4
Recent Votes
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
C: Reads mapped to another chromosome in paired-end data of RNA-seq
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Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
bk11
★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
• 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
by
ATpoint
82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> have two bed files these are not bed files. A chromosome is missing in chromosome 1 > How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
by
GenoMax
142k
Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks. In theory if you are aligning …
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Arton
▴ 10
Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
DBScan
▴ 300
I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
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