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12,524 results • Page 2 of 251
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10
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33
replies
3.9k
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Looking for a tool like fastq screen but for ONT data
gridion nanopore ont minion
updated 11 months ago by 43k • written 5.8 years ago by ★ 1.4k
120
votes
31
replies
200k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 6 months ago by 43k • written 14.1 years ago by 11k
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.4 years ago by ▴ 320
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 5 months ago by ▴ 450 • written 12.9 years ago by ★ 5.1k
11
votes
31
replies
15k
views
6 follow
How to concatenate multiple fasta file
sequence genome
updated 11 months ago by • 0 • written 5.8 years ago by ▴ 50
147
votes
31
replies
138k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 9 months ago by 43k • written 12.2 years ago by ★ 2.9k
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 6 months ago by 43k • written 14.2 years ago by ★ 1.0k
31
votes
30
replies
15k
views
6 follow
Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene RNA-Seq Venn-diagram PCA
updated 11 months ago by 43k • written 6.0 years ago by ▴ 450
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 7 weeks ago by 100k • written 8.2 years ago by 43k
18
votes
30
replies
10k
views
6 follow
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina BBMap filterbytile
updated 10 months ago by 43k • written 7.4 years ago by 20k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 6 months ago by 43k • written 14.1 years ago by 18k
16
votes
29
replies
1.8k
views
Gene labels problem in enhanced volcano
R ggplot2 enhancedvolcano
updated 3 months ago by ★ 27k • written 3 months ago by ▴ 120
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 10 months ago by • 0 • written 8.2 years ago by 20k
4
votes
29
replies
11k
views
6 follow
WGCNA soft thresholding problem
WGCNA RNA-Seq soft thresholding data normalization
updated 12 weeks ago by ▴ 10 • written 5.5 years ago by ▴ 40
20
votes
29
replies
2.5k
views
6 follow
Using bcftools to find unique alt homozygous sites
bcftools
updated 7 months ago by 161k • written 7 months ago by ▴ 70
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 9 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
124
votes
29
replies
7.4k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 6 months ago by 43k • written 14.2 years ago by 7.4k
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 16 days ago by • 0 • written 12.8 years ago by ★ 1.7k
43
votes
28
replies
5.7k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 6 months ago by 43k • written 14.1 years ago by 11k
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
3 months ago by Jeremy Leipzig 22k
3
votes
27
replies
2.6k
views
7 follow
Forum: What server do you use?
HPC AWS
updated 12 months ago by 43k • written 5.8 years ago by ★ 1.9k
197
votes
27
replies
35k
views
20 follow
Forum: Bioinformatics Cartoon
bioinformatics
updated 10 months ago by 43k • written 12.4 years ago by ★ 2.3k
28
votes
27
replies
15k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython python fastq next-gen-sequencing
updated 6 months ago by 43k • written 14.1 years ago by 4.6k
82
votes
27
replies
21k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq atac-seq normalization
updated 6 weeks ago by • 0 • written 4.4 years ago by ▴ 250
27
votes
27
replies
10k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp allele biomart dbsnp
updated 6 months ago by 43k • written 14.2 years ago by 54k
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by • 0 • written 10.3 years ago by 100k
26
votes
27
replies
2.2k
views
10 follow
Forum: Determining computer time required
computer hpc time
updated 4 months ago by ★ 6.0k • written 4 months ago by ▴ 40
77
votes
26
replies
121k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 5 months ago by ★ 2.8k • written 9.1 years ago by ▴ 260
24
votes
26
replies
3.7k
views
Tool: ClinCNV: CNV detection from short reads
variant-calling cna cnv
updated 11 months ago by 43k • written 4.6 years ago by ★ 2.9k
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq ChIP-Seq GO gene ontology
written 8.2 years ago by ▴ 370
21
votes
26
replies
9.8k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 9 weeks ago by ▴ 30 • written 4.5 years ago by 8.6k
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 8 months ago by 11k • written 11.3 years ago by ▴ 810
47
votes
26
replies
4.2k
views
11 follow
Blog: Evolution of Biostars
meta Biostars
updated 8 months ago by ▴ 70 • written 5.2 years ago by 7.1k
3
votes
26
replies
2.0k
views
6 follow
STAR Genome index Error
STAR
updated 7 months ago by 43k • written 7 months ago by • 0
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 6 months ago by 43k • written 14.2 years ago by 13k
20
votes
26
replies
3.3k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment fasta image
updated 9 months ago by 21k • written 4.9 years ago by ▴ 210
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 6 months ago by 43k • written 14.1 years ago by 161k
7
votes
25
replies
11k
views
6 follow
Tool: MIGEC: towards error-free profiling of immune repertoires
sequencing-error tcr antibody molecular-barcode
updated 10 months ago by 43k • written 10.0 years ago by 3.5k
69
votes
25
replies
7.1k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 6 months ago by 43k • written 14.2 years ago by ▴ 190
13
votes
25
replies
11k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis sequencing ngs
updated 10 months ago by 43k • written 10.8 years ago by 3.5k
60
votes
25
replies
5.8k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size statistical-power RNA-Seq
updated 11 months ago by 43k • written 3.8 years ago by ▴ 230
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen RNA-Seq
updated 4 months ago by ▴ 60 • written 9.7 years ago by ▴ 90
18
votes
25
replies
15k
views
13 follow
Easy way to split VCF file by chromosome
sequence TOPMED chromosome Imputation SNP
updated 10 months ago by 161k • written 2.3 years ago by ▴ 30
13
votes
25
replies
4.4k
views
7 follow
VEP output has no gene names
alignment sequencing vep
updated 11 months ago by ★ 2.2k • written 5.8 years ago by ▴ 240
38
votes
25
replies
9.2k
views
13 follow
FASTA file of fixed length
sequence fasta
updated 8 months ago by 43k • written 8.1 years ago by ▴ 250
6
votes
25
replies
39k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 11 months ago by • 0 • written 6.2 years ago by ▴ 130
68
votes
25
replies
16k
views
12 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 6 months ago by 142k • written 5.2 years ago by ★ 1.4k
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general subjective
updated 7 months ago by 43k • written 14.3 years ago by 28k
51
votes
25
replies
6.9k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 6 months ago by 43k • written 14.2 years ago by 54k
17
votes
25
replies
2.5k
views
Tool: Platform for Bioinformatics Students, Scholars and Scientists
sequence genome
updated 10 months ago by 43k • written 8.2 years ago by ▴ 50
12,524 results • Page 2 of 251
Recent Votes
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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Recent Replies
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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