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402 results • Page 1 of 9
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144
votes
69
replies
43k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 1 day ago by ▴ 10 • written 5.4 years ago by 85k
138
votes
42
replies
20k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 4 days ago by ★ 2.6k • written 9.8 years ago by ★ 1.6k
79
votes
34
replies
7.7k
views
15 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 14 hours ago by 38k • written 7.4 years ago by ▴ 650
31
votes
34
replies
5.7k
views
11 follow
Forum: pros- and cons- : programming skills vs. GUI
programming lecture
updated 13 hours ago by 38k • written 7.3 years ago by ★ 4.6k
18
votes
31
replies
5.7k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff parse
updated 3 days ago by 7.8k • written 4.5 years ago by ▴ 350
50
votes
30
replies
10k
views
8 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP genotype GATK
updated 18 hours ago by • 0 • written 5.1 years ago by ▴ 490
49
votes
28
replies
25k
views
12 follow
Trimming A Fastq File Representing Rna-Seq Data
fastq RNA-seq
updated 4 days ago by 38k • written 11.0 years ago by ★ 1.2k
49
votes
27
replies
6.0k
views
10 follow
Forum: Possible augmented reality tools for bioinformatics and current problems
visualization 3D augmented-reality
updated 1 day ago by 38k • written 7.4 years ago by ▴ 90
11
votes
25
replies
5.0k
views
15 follow
News: Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted with the NCBI_NOW Tag
NCBI_NOW
updated 1 day ago by 38k • written 7.5 years ago by ▴ 320
7
votes
16
replies
2.0k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 4 days ago by 38k • written 5.5 years ago by ★ 3.6k
20
votes
15
replies
4.8k
views
7 follow
Experience With Parser Generators For Common Formats
parser
updated 4 days ago by 38k • written 10.1 years ago by ★ 1.3k
5
votes
15
replies
3.2k
views
Blast+ Error Code=12
blast
updated 4 days ago by 38k • written 11.2 years ago by ▴ 160
12
votes
15
replies
4.3k
views
7 follow
ACMG assignment tools
wes acmg WES WGS
updated 4 days ago by ▴ 30 • written 2.8 years ago by ▴ 170
21
votes
12
replies
9.8k
views
7 follow
An Alternative To Rsync (Or Useful Parameters)
next-gen-sequencing
updated 4 days ago by 38k • written 11.5 years ago by 4.3k
2
votes
11
replies
9.2k
views
9 follow
CD-HIT Clustering output
Clustering CD-HIT
updated 3 days ago by ▴ 10 • written 8.7 years ago by • 0
4
votes
11
replies
457
views
Align miRNA library (small RNA-seq) without trimming
BOWTIE2 RNA-SEQ BOWTIE
1 day ago by Paola ▴ 10
3
votes
10
replies
4.1k
views
Make A Special File By Plink
plink ped
updated 4 days ago by 38k • written 9.4 years ago by ▴ 210
8
votes
10
replies
593
views
7 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming Masters
updated 3 days ago by ▴ 730 • written 10 days ago by • 0
10
votes
10
replies
14k
views
7 follow
Is the heterozygosity flag (--het) in vcftools calculate observed and expected heterozygosity?
vcftools vcf
updated 4 days ago by 85k • written 5.7 years ago by ▴ 40
6
votes
10
replies
3.8k
views
Tool: Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 5 days ago by 38k • written 7.1 years ago by ▴ 350
6
votes
9
replies
6.7k
views
8 follow
Any methods available to do QC analysis of Pacbio raw data??
Assembly genome Pacbio next-gen sequencing
updated 3 days ago by • 0 • written 5.5 years ago by ▴ 120
3
votes
9
replies
2.9k
views
Need recommendation for a virtual machine or linux cluster for ngs analysis
ngs
updated 13 hours ago by 38k • written 7.4 years ago by ▴ 220
7
votes
9
replies
756
views
Aberrant splicing in bulk RNAseq
aberrant-splicing transcript isoform exon
updated 2 days ago by ★ 4.0k • written 6 weeks ago by ▴ 70
12
votes
9
replies
735
views
6 follow
How to find promoter sequence of a gene?
promoter
3 days ago by sunyeping ▴ 80
2
votes
9
replies
1.4k
views
snpEff: ERROR_CHROMOSOME_NOT_FOUND
variant annotation
updated 1 day ago by • 0 • written 14 months ago by ▴ 10
1
vote
8
replies
696
views
If RNA-seq includes miRNA genes then why are there miRNA specific pipelines?
RNA miRNA sequencing RNA-seq
1 day ago by Kermit ▴ 80
2
votes
8
replies
5.2k
views
Cel File Not Available. Extracting Cel File Information From The Txt File.
microarray
updated 4 days ago by 38k • written 10.6 years ago by • 0
3
votes
8
replies
3.8k
views
counting the unmapped reads
RNA-Seq
updated 4 days ago by • 0 • written 7.9 years ago by ★ 4.1k
0
votes
8
replies
402
views
How to get subset of a Seurat object based on metadata?
scRNA-seq Seurat
updated 1 day ago by ▴ 940 • written 2 days ago by ▴ 80
2
votes
8
replies
9.1k
views
Size of typical genomic data
genomic
updated 4 days ago by 38k • written 4.9 years ago by 10k
10
votes
8
replies
461
views
7 follow
Forum: Any tips in landing a bioinformatic job?
Spain R
1 day ago by Jorge ▴ 30
4
votes
8
replies
6.4k
views
SNPs located in promoter region. OR exon, intron, 5'UTR, 3'UTR
SNP
updated 13 hours ago by 38k • written 7.3 years ago by • 0
11
votes
8
replies
590
views
6 follow
split fasta file to train deep learning model
fasta split bash R
updated 4 days ago by 8.0k • written 12 days ago by ▴ 10
33
votes
8
replies
32k
views
9 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 2 days ago by • 0 • written 6.4 years ago by ▴ 500
13
votes
8
replies
13k
views
Sam To Bed File With Counter Column
bed sam
updated 4 days ago by 38k • written 10.2 years ago by ▴ 90
5
votes
8
replies
1.5k
views
DiffBind missing peaks and FRiP
DiffBind ChIP-seq
updated 22 hours ago by ★ 1.7k • written 13 months ago by ▴ 20
15
votes
8
replies
3.7k
views
Forum: Asking for opinions about Bioinformatics Data Skills book
book
updated 1 day ago by 38k • written 7.7 years ago by 11k
6
votes
7
replies
4.4k
views
Creation Of A .Bed File From .Txt
plink
updated 4 days ago by 38k • written 9.2 years ago by • 0
2
votes
7
replies
690
views
Size of Proteins (Acetohalobium arabaticum - species)
protein python
updated 4 days ago by 38k • written 3 months ago by • 0
3
votes
7
replies
218
views
What is the major problem with this pipeline of SNPs analysis?
Genomics Fungi SNP VCF
updated 17 hours ago by 38k • written 19 hours ago by • 0
5
votes
7
replies
394
views
Most efficient way to run Diamond against a very very large database (i.e., NCBI's NR)?
protein annotation alignment diamond nr
3 days ago by O.rka ▴ 650
3
votes
7
replies
273
views
1000 genomes hg38 with dbSNP rsid
1000genomes dbsnp
updated 4 days ago by 38k • written 4 days ago by ▴ 150
1
vote
7
replies
2.4k
views
Forum: Bioinformatics & Virology or Immunology.
immunology virology
updated 14 hours ago by 38k • written 7.4 years ago by • 0
6
votes
7
replies
1.1k
views
The size of the genome in pb of an organism before sequencing?
sequencing genome
updated 4 days ago by 38k • written 4.4 years ago by • 0
1
vote
7
replies
477
views
Dependent p values
pvalue snp Gene
52 minutes ago by Eliza ▴ 20
20
votes
7
replies
3.1k
views
Forum: Change career path
education career
updated 16 hours ago by 38k • written 7.4 years ago by ▴ 40
10
votes
7
replies
1.1k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
2 days ago by barslmn ★ 1.4k
2
votes
7
replies
3.5k
views
error in downloading of some accesions with fastq-dump
fastq-dump
updated 6 days ago by • 0 • written 9 months ago by ▴ 50
5
votes
7
replies
1.9k
views
How to obtain the non-redundant total size of the GRCh38 genome?
exome
updated 4 days ago by 38k • written 6.3 years ago by ▴ 10
10
votes
7
replies
2.8k
views
Binning fasta sequences by size?
fasta
updated 4 days ago by 38k • written 5.2 years ago by ▴ 40
402 results • Page 1 of 9
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Replies
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p by Daniel • 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
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