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Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
updated 18 minutes ago by • 0 • written 8.2 years ago by • 0
2
votes
7
replies
5.0k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated just now by 81k • written 7.1 years ago by ▴ 80
1
vote
0
replies
27
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor
Bioconductor versions R Rstudio
1 hour ago by BioinfGuru ★ 1.7k
1
vote
1
reply
235
views
Plink merge errors.
cygwin64 bed PLINK
2 hours ago by Dinmukhamed • 0
0
votes
0
replies
25
views
Conversion to tree format
PLINK Figtree file .bed SplitsTree
2 hours ago by Dinmukhamed • 0
0
votes
0
replies
51
views
miRDeep2: How to get the read counts
mirdeep2
4 hours ago by Atul K. • 0
1
vote
2
replies
274
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 5 hours ago by 161k • written 17 hours ago by • 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 2.6k • written 7.4 years ago by 100k
0
votes
0
replies
63
views
Lncipedia GTF file error
Proteomics Bioinformatics
6 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 6 hours ago by 6.3k • written 15 months ago by ▴ 130
3
votes
1
reply
157
views
Free/open source 23andme-like analysis
NGS SNPs genomics VCF
updated 5 hours ago by 54k • written 10 hours ago by ▴ 510
0
votes
2
replies
368
views
How to get the reference panel for UKBB
UKBB GWAS clump
13 hours ago by 航太郎 • 0
0
votes
2
replies
239
views
Adding CB tag to bam file
samtools bam
5 hours ago by Maria • 0
11
votes
12
replies
729
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 15 hours ago by 43k • written 21 hours ago by • 0
0
votes
0
replies
92
views
create genewise sync file in popoolation
popoolation
updated 17 hours ago by 141k • written 18 hours ago by • 0
0
votes
2
replies
233
views
python file for coding potential calculator
cpc2.py
10 hours ago by Ashok • 0
0
votes
2
replies
229
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
10 hours ago by Ashok • 0
0
votes
2
replies
251
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
8 hours ago by Ashok • 0
5
votes
2
replies
343
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
updated 21 hours ago by ★ 1.2k • written 1 day ago by ▴ 40
0
votes
0
replies
97
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 22 hours ago by 43k • written 22 hours ago by • 0
1
vote
1
reply
260
views
Problem with Mirdeep2 and Randfold output
mirdeep2 Randfold
22 hours ago by otieno43 ▴ 30
0
votes
1
reply
179
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
updated 22 hours ago by 43k • written 22 hours ago by ▴ 10
0
votes
0
replies
104
views
traying to make a maf from an already annotated vcf
vcf2maf VEP maftools
updated 22 hours ago by 43k • written 22 hours ago by • 0
1
vote
4
replies
594
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 22 hours ago by 43k • written 3 months ago by • 0
0
votes
0
replies
97
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
105
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
18 hours ago by Chris ▴ 260
0
votes
0
replies
110
views
News: Online course: Meta-analysis in R
Meta-Analysis Statistics R
updated 23 hours ago by 43k • written 1 day ago by ★ 2.5k
1
vote
9
replies
642
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 1 day ago by ★ 2.4k • written 1 day ago by • 0
0
votes
1
reply
192
views
10x VDJ (TCR/BCR) BAM to fastq
TCR VDJ BCR 10x
updated 1 day ago by 141k • written 1 day ago by ★ 1.9k
0
votes
1
reply
209
views
DEseq2
RNA-seq DESeq2
updated 23 hours ago by 43k • written 1 day ago by • 0
0
votes
0
replies
111
views
News: Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo Individual-Based-Models Agent-Based-Models
updated 23 hours ago by 43k • written 1 day ago by ★ 2.5k
4
votes
2
replies
267
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 1 day ago by 8.5k • written 1 day ago by ▴ 20
1
vote
0
replies
112
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
1 day ago by Novogene ▴ 420
0
votes
1
reply
382
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 23 hours ago by 43k • written 19 months ago by • 0
3
votes
3
replies
381
views
Korean human genome reference file
GWAS reference imputation
9 hours ago by SeoGyun • 0
3
votes
4
replies
390
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
updated 1 day ago by 141k • written 1 day ago by • 0
0
votes
3
replies
349
views
RNA seq differential expression analysis
RNA-seq normalization
updated 15 hours ago by 14k • written 1 day ago by • 0
0
votes
0
replies
113
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 23 hours ago by 43k • written 1 day ago by ▴ 10
0
votes
0
replies
127
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
128
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
1 day ago by ekirsch • 0
0
votes
1
reply
265
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
updated 13 hours ago by ★ 3.8k • written 1 day ago by • 0
1
vote
1
reply
217
views
Pediococcus acidilactici sequence analysis
BLAST Gene-Ontology
updated 1 day ago by 43k • written 1 day ago by ▴ 120
3
votes
1
reply
575
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 1 day ago by ▴ 20 • written 19 months ago by ★ 4.3k
0
votes
0
replies
131
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
224
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 1 day ago by 141k • written 1 day ago by • 0
5
votes
4
replies
545
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
243
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf bam bcf snps
updated 1 day ago by 3.9k • written 1 day ago by ▴ 10
0
votes
4
replies
472
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
7 hours ago by Kai Xin • 0
1
vote
1
reply
200
views
Retrieve a % coverage for each transcript
RNA-seq
updated 1 day ago by 43k • written 1 day ago by ▴ 40
0
votes
1
reply
318
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 1 day ago by ▴ 150 • written 7 days ago by ▴ 40
116,478 results • Page 1 of 2330
Recent Votes
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
A: Read counts of STAR with gff file
Comment: Free/open source 23andme-like analysis
A: How to obtain all accession.version identifiers for a BLAST database using ENTRE
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Recent Replies
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
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
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