Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
117,080 results • Page
2 of 2342
Sort: Rank
Rank
Views
Votes
Replies
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
225
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
89
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 22 hours 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
203
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
1 day 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 1 day ago by
Ram
44k • written 1 day ago by
Harshita
• 0
2
votes
4
replies
237
views
Filter Genome for Specific Sites
bedtools
updated 1 day ago by
Ram
44k • written 2 days ago by
Anita
• 0
0
votes
3
replies
246
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 1 day 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 1 day 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 22 hours ago by
jared.andrews07
★ 17k • written 20 days ago by
Oburah
• 0
0
votes
2
replies
180
views
vcf phasing
beagle
WhatsHap
phasing
10 hours ago by
safeassli
▴ 10
0
votes
2
replies
204
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
1 day ago by
sainavyav22
• 0
0
votes
1
reply
606
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
190
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
199
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
105
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
153
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 1 day 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
147
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
248
views
GO analysis: p-value range
GO
R
updated 2 days ago by
Matthias Zepper
4.6k • written 2 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 2 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
102
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
2 days ago by
Maryam
• 0
0
votes
4
replies
337
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
2 days ago by
Bibi
• 0
1
vote
2
replies
355
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 2 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
322
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 1 day 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
727
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
381
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 22 hours 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
0
votes
0
replies
148
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
4 days ago by
Moinuddin
• 0
0
votes
1
reply
189
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Jacek
▴ 20
2
votes
1
reply
260
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 3 days ago by
Gordon Smyth
★ 7.2k • written 4 days ago by
marineandriot
• 0
0
votes
0
replies
149
views
How can i use ESM-1v ?
VEP
ESM-1v
4 days ago by
Meto
• 0
0
votes
0
replies
160
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Long
• 0
2
votes
3
replies
342
views
Trimming tool
Trimming
updated 1 day ago by
Ram
44k • written 4 days ago by
GeneC
• 0
0
votes
0
replies
152
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
4 days ago by
kilcdincer
▴ 10
117,080 results • Page
2 of 2342
Recent Votes
C: Classifying normal vs cancer tissues from mutational data
Classifying normal vs cancer tissues from mutational data
Pymol Scripting Help
A: Not sure if pipe from bowtie2 to samtools is working?
Comment: FastQC interpretation - 16S sequencing
Comment: FastQC interpretation - 16S sequencing
Answer: vg autoindex seems stuck after a week of running
Recent Locations •
All
Vietnam,
1 minute ago
United States,
1 minute ago
France,
1 minute ago
Hong Kong,
5 minutes ago
United States,
6 minutes ago
United States,
7 minutes ago
USA,
9 minutes ago
Recent Awards •
All
Popular Question
to
Wilber0x
▴ 50
Scholar
to
Ashutosh Pandey
12k
Popular Question
to
pinheirofabiano
▴ 20
Popular Question
to
andres_arroyo
• 0
Popular Question
to
Tawny
▴ 180
Popular Question
to
anasjamshed
▴ 120
Student
to
Rafael Soler
★ 1.2k
Recent Replies
Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing
by
Christopher
• 0
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
But I used the same bam files in both freebayes and GATK. Even the overlapping SNPs from both software are giving different estimates in te…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
Pierre Lindenbaum
162k
may be downsampling(?), QC failing reads ?
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
Thank you. However, I extracted the AD for each SNP that gives two numbers separated by a comma. I guess the first one is for reference and…
Answer: How to get the ratio of allele counts from GATK derived VCF file?
by
Pierre Lindenbaum
162k
> However, I am doing SNP calling using GATK, but there is no such information field for reference and alternate allele counts. it's in …
Comment: samtools write-index
by
GenoMax
142k
> The index file is older than the data file: alignment.sorted.bam.bai I don't think that warning is going to cause any issues. Not sure w…
Comment: samtools write-index
by
Pierre Lindenbaum
162k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o alignment.sorted.bam` should be enoug…
Answer: from CRAM to fastq
by
Pierre Lindenbaum
162k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq
by
machaalani29
• 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq
by
machaalani29
• 0
the option -c is to compress the file
Comment: from CRAM to fastq
by
GenoMax
142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R
by
GenoMax
142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
Activities with `cucurbitacin A`: https://www.ebi.ac.uk/chembl/web_components/explore/activities/STATE_ID:RHxG8uDfrtbmiyaY55ic-w%3D%3D `cu…
Traffic: 2533 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6