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1,000 results • Page 4 of 20
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13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 2 days ago by 43k • written 6.8 years ago by ★ 1.3k
138
votes
22
replies
65k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 10 months ago by 87k • written 6.4 years ago by ★ 1.9k
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 9 months ago by • 0 • written 11.0 years ago by ▴ 90
9
votes
22
replies
9.6k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
9 months ago by vytarasov ▴ 180
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 9 days ago by 43k • written 5.0 years ago by ▴ 260
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 10 months ago by 43k • written 8.0 years ago by 13k
39
votes
21
replies
13k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 10 months ago by 43k • written 5.5 years ago by 8.5k
18
votes
21
replies
4.4k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 9 months ago by 43k • written 7.1 years ago by 13k
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by • 0 • written 10.0 years ago by ▴ 660
16
votes
21
replies
9.9k
views
7 follow
How to extract bigWig signal for a given bed file?
bigWig
updated 8 months ago by 43k • written 7.5 years ago by ▴ 60
13
votes
21
replies
1.7k
views
Practical Haplotype Graph Paths
practical-haplotype-graph PHG
updated 10 weeks ago by ▴ 200 • written 5 months ago by ▴ 10
4
votes
21
replies
2.6k
views
Limma returned only positive logFC values
edgeR differential-expression deg limma
10 months ago by melissachua90 ▴ 60
4
votes
21
replies
2.3k
views
6 follow
how to automate this process
python plantCARE
updated 9 months ago by 43k • written 7.2 years ago by ▴ 680
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by ▴ 70 • written 9.8 years ago by ▴ 170
22
votes
21
replies
4.8k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 5 months ago by 43k • written 14.0 years ago by 18k
14
votes
21
replies
10k
views
7 follow
HOMER annotatePeaks.pl problem
RNA-Seq ChIP-Seq HOMER
updated 10 months ago by 43k • written 6.6 years ago by ▴ 110
5
votes
21
replies
2.9k
views
How to get my tool on Homebrew ?
homebrew pipeline
updated 10 months ago by 43k • written 4.8 years ago by ▴ 20
13
votes
21
replies
3.0k
views
6 follow
Aberrant splicing in bulk RNAseq
aberrant-splicing transcript isoform exon
updated 10 months ago by • 0 • written 14 months ago by ▴ 110
15
votes
21
replies
5.5k
views
7 follow
alphafold online availability and use case
alphafold structure prediction
written 2.7 years ago by ▴ 70
60
votes
21
replies
3.8k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome assembly
updated 7 months ago by 54k • written 7 months ago by ▴ 60
43
votes
21
replies
5.4k
views
9 follow
Helping Biostar Grow
biostars
updated 5 months ago by 43k • written 14.0 years ago by 11k
23
votes
21
replies
8.8k
views
9 follow
fastest UMAP method
UMAP R
updated 5 months ago by ★ 27k • written 4.5 years ago by ▴ 30
0
votes
21
replies
1.0k
views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
10 weeks ago by analyst ▴ 20
10
votes
21
replies
3.2k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq deeptools
8 months ago by Chris ▴ 260
12
votes
21
replies
6.6k
views
7 follow
Illumina HumanHT-12 V4.0 expression beadchip
R lumi LIMMA
updated 5 months ago by ★ 7.0k • written 4.0 years ago by ▴ 50
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 9 months ago by 43k • written 12.0 years ago by ★ 1.5k
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 7 months ago by ▴ 210 • written 10.2 years ago by ▴ 750
24
votes
21
replies
7.5k
views
9 follow
News: Misunderstood parameter of NCBI BLAST
blast alignment
updated 10 months ago by 43k • written 5.6 years ago by ★ 3.4k
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 5 months ago by 43k • written 14.0 years ago by 4.9k
21
votes
20
replies
9.1k
views
11 follow
Laptops for bioinformatics
hardware Laptops
updated 10 months ago by 4.2k • written 17 months ago by ▴ 40
16
votes
20
replies
14k
views
7 follow
Extracting allele, Genotype from VCF file
vcf
updated 10 months ago by 43k • written 6.0 years ago by ▴ 20
7
votes
20
replies
6.3k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 7 days ago by ▴ 190 • written 4.3 years ago by ▴ 80
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 9 months ago by ▴ 30 • written 13.5 years ago by ▴ 470
7
votes
20
replies
2.0k
views
Forum: NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR RNA-Seq TopHat
updated 11 months ago by 43k • written 3.3 years ago by ▴ 10
15
votes
20
replies
1.7k
views
Bbtools callvariant multisample mode, + base recalibration
Bbtools
4 months ago by Axzd ▴ 70
18
votes
20
replies
4.1k
views
9 follow
Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Different Populations Of Cicadas?
project education
updated 5 months ago by 43k • written 14.1 years ago by ▴ 70
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 3 months ago by 11k • written 8.3 years ago by ▴ 80
14
votes
20
replies
6.6k
views
7 follow
Tool Recommendations For Human Genome Assembly
assembly human-genome
updated 10 months ago by 43k • written 11.1 years ago by ▴ 800
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper RNA-seq
6 months ago by langziv ▴ 50
17
votes
20
replies
1.4k
views
What is the best way to compute genetic distances between FASTQ files?
genetic-distance fastq
updated 5 months ago by 141k • written 5 months ago by ▴ 10
37
votes
20
replies
7.2k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 5 months ago by 43k • written 14.0 years ago by 11k
29
votes
20
replies
3.6k
views
Tool: FastQt : a clone of FastQC in C++/Qt
fastqc Cpp fastq Qt
updated 9 months ago by 43k • written 7.4 years ago by ★ 2.4k
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 9 days ago by 43k • written 6.2 years ago by ▴ 90
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 9 days ago by 43k • written 7.5 years ago by ▴ 80
49
votes
20
replies
2.0k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 3 months ago by ★ 2.6k • written 3 months ago by ★ 27k
12
votes
20
replies
2.2k
views
Is there a single header file somewhere I can use to read bam?
cpp bam c
updated 11 months ago by 43k • written 5.5 years ago by ▴ 720
22
votes
20
replies
4.8k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 10 months ago by 43k • written 5.5 years ago by ▴ 150
2
votes
20
replies
2.3k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
7 months ago by Maxine ▴ 40
12
votes
20
replies
2.4k
views
SEACR and MACS2
MACS2 SEACR
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 10
12
votes
20
replies
1.2k
views
Help with gatk BaseRecalibrator
GATK variant-calling
updated 4 months ago by 43k • written 4 months ago by ▴ 260
1,000 results • Page 4 of 20
Recent Votes
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
Filtration Of Reads With Length Lower Than 30 From Bam
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
Answer: How to compare the quality of assemblies
Comment: How to compare the quality of assemblies
Bedtools merge but only if intersection exists
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Popular Question to Michael 54k
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Recent Replies
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't amongst your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry a…
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 ▴ 150
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/…
Comment: How to get the reference panel for UKBB by 航太郎 • 0
Thanks for your guide!
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you so much
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