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116,478 results • Page
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Could you please assist in identifying this cluster?
cell
single
updated 28 minutes ago by
ATpoint
81k • written 29 minutes ago by
Kazo
• 0
4
votes
9
replies
2.5k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
updated 1 hour ago by
a.l.b.e.r.to.2.5.s.an.ic.s.
• 0 • written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.0k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 39 minutes ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
1
vote
0
replies
33
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor
Bioconductor
versions
R
Rstudio
2 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
252
views
Plink merge errors.
cygwin64
bed
PLINK
2 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
37
views
Conversion to tree format
PLINK
Figtree
file
.bed
SplitsTree
2 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
55
views
miRDeep2: How to get the read counts
mirdeep2
4 hours ago by
Atul K.
• 0
1
vote
2
replies
280
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 6 hours ago by
Pierre Lindenbaum
161k • written 17 hours ago by
rahu
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
65
views
Lncipedia GTF file error
Proteomics
Bioinformatics
7 hours ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.6k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 7 hours ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
2
replies
171
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
31 minutes ago by
joe
▴ 510
0
votes
2
replies
372
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
14 hours ago by
航太郎
• 0
0
votes
2
replies
245
views
Adding CB tag to bam file
samtools
bam
5 hours ago by
Maria
• 0
11
votes
12
replies
736
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 16 hours ago by
Ram
43k • written 22 hours ago by
iamsmor
• 0
0
votes
0
replies
93
views
create genewise sync file in popoolation
popoolation
updated 17 hours ago by
GenoMax
141k • written 18 hours ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
236
views
python file for coding potential calculator
cpc2.py
10 hours ago by
Ashok
• 0
0
votes
2
replies
233
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
11 hours ago by
Ashok
• 0
0
votes
2
replies
253
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
8 hours ago by
Ashok
• 0
5
votes
2
replies
347
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 22 hours ago by
shelkmike
★ 1.2k • written 1 day ago by
kirillkirilenko
▴ 40
0
votes
0
replies
100
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 22 hours ago by
Ram
43k • written 22 hours ago by
samuelkalandarov2002
• 0
1
vote
1
reply
261
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
23 hours ago by
otieno43
▴ 30
0
votes
1
reply
181
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 22 hours ago by
Ram
43k • written 23 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
106
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 23 hours ago by
Ram
43k • written 23 hours ago by
Javier
• 0
1
vote
4
replies
595
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 23 hours ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
99
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
23 hours ago by
enferdeflame
• 0
0
votes
0
replies
108
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
19 hours ago by
Chris
▴ 260
0
votes
0
replies
114
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
1
vote
9
replies
648
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 1 day ago by
Elisabeth Gasteiger
★ 2.4k • written 1 day ago by
Jacky
• 0
0
votes
1
reply
194
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 1 day ago by
GenoMax
141k • written 1 day ago by
predeus
★ 1.9k
0
votes
1
reply
211
views
DEseq2
RNA-seq
DESeq2
updated 1 day ago by
Ram
43k • written 1 day ago by
rrehimi
• 0
0
votes
0
replies
113
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
4
votes
2
replies
270
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 1 day ago by
Juke34
8.5k • written 1 day ago by
njornet
▴ 20
1
vote
0
replies
114
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
1 day ago by
Novogene
▴ 420
0
votes
1
reply
383
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 1 day ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
3
votes
3
replies
386
views
Korean human genome reference file
GWAS
reference
imputation
10 hours ago by
SeoGyun
• 0
3
votes
4
replies
393
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 1 day ago by
GenoMax
141k • written 1 day ago by
n_navy
• 0
0
votes
3
replies
356
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 15 hours ago by
swbarnes2
14k • written 1 day ago by
rrehimi
• 0
0
votes
0
replies
115
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 1 day ago by
Ram
43k • written 1 day ago by
bioinfo223
▴ 10
0
votes
0
replies
128
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
1 day ago by
P.
• 0
0
votes
0
replies
130
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
1 day ago by
ekirsch
• 0
0
votes
1
reply
268
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
updated 13 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
renan.igor
• 0
1
vote
1
reply
218
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 1 day ago by
Ram
43k • written 1 day ago by
anasjamshed
▴ 120
3
votes
1
reply
576
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 1 day ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
132
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
1 day ago by
synat.keam
▴ 100
0
votes
1
reply
225
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
ycts
• 0
5
votes
4
replies
549
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
18 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
244
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 1 day ago by
LChart
3.9k • written 1 day ago by
George
▴ 10
0
votes
4
replies
475
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
8 hours ago by
Kai Xin
• 0
1
vote
1
reply
201
views
Retrieve a % coverage for each transcript
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
jammydodger123456
▴ 40
116,478 results • Page
1 of 2330
Recent Votes
Answer: Problem with Sniffles pipeline and SV calling help
Illumina reads preprocessing best practice for snp calling applications
Comment: Illumina reads preprocessing best practice for snp calling applications
Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Basic normalization, batch correction and visualization of RNA-seq data
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Comment: Illumina reads preprocessing best practice for snp calling applications
by
Enrique
• 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster?
by
ATpoint
81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis
by
joe
▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort
by
ATpoint
81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files
by
Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort
by
tamas.malkocs
• 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
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