Limit : this year
all time today this week this month this year
1,000 results • Page 2 of 20
Sort: Votes
Rank Views Votes Replies
129
votes
22
replies
52k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 4 days ago by 85k • written 5.6 years ago by ★ 1.8k
129
votes
38
replies
6.0k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 9 days ago by 39k • written 4.2 years ago by 98k
128
votes
33
replies
56k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 7 months ago by 39k • written 9.1 years ago by ▴ 480
126
votes
44
replies
28k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 3 months ago by 39k • written 6.7 years ago by ▴ 970
125
votes
46
replies
44k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 9 weeks ago by 39k • written 7.3 years ago by ★ 3.2k
122
votes
42
replies
9.0k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 3 months ago by 39k • written 10.5 years ago by 98k
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 3 months ago by 39k • written 13.0 years ago by 5.3k
120
votes
53
replies
91k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 11 weeks ago by • 0 • written 9.0 years ago by ▴ 330
120
votes
33
replies
36k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 4 weeks ago by ★ 2.3k • written 9.8 years ago by 11k
118
votes
26
replies
33k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 3 months ago by ▴ 50 • written 8.1 years ago by ▴ 610
117
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 7 months ago by 130k • written 12.5 years ago by ★ 3.3k
117
votes
59
replies
30k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 4 months ago by 39k • written 8.1 years ago by ▴ 30
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 12 weeks ago by 39k • written 4.9 years ago by 72k
116
votes
35
replies
7.2k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 3 months ago by 39k • written 10.2 years ago by 21k
115
votes
35
replies
38k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 27 days ago by 39k • written 6.0 years ago by ▴ 760
114
votes
25
replies
65k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 4 months ago by ▴ 10 • written 12.4 years ago by 154k
113
votes
53
replies
5.3k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 9 days ago by 39k • written 4.2 years ago by ▴ 170
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 9 months ago by 39k • written 12.1 years ago by ▴ 480
110
votes
37
replies
7.1k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 3 months ago by 39k • written 11.7 years ago by 154k
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 8 months ago by 39k • written 11.0 years ago by ▴ 380
106
votes
45
replies
82k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 9 months ago by ▴ 30 • written 10.9 years ago by ▴ 320
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 3 months ago by 39k • written 9.3 years ago by ▴ 590
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 3 months ago by 39k • written 9.8 years ago by ★ 1.1k
105
votes
26
replies
39k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 8 months ago by 39k • written 10.4 years ago by ▴ 810
104
votes
12
replies
73k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 7 months ago by 39k • written 11.6 years ago by ★ 1.7k
102
votes
44
replies
7.9k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 3 months ago by 39k • written 9.8 years ago by 24k
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 11 months ago by 39k • written 13.3 years ago by ★ 1.0k
102
votes
81
replies
25k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 9 months ago by 130k • written 6.4 years ago by ★ 1.9k
102
votes
19
replies
17k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 3 months ago by 39k • written 11.0 years ago by ▴ 830
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 12 weeks ago by 39k • written 4.8 years ago by 16k
101
votes
31
replies
84k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 11 months ago by 39k • written 11.9 years ago by ★ 5.0k
100
votes
15
replies
100k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 3 months ago by ▴ 20 • written 11.0 years ago by 12k
100
votes
38
replies
28k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 4 weeks ago by 21k • written 9.6 years ago by ★ 3.6k
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 9 weeks ago by 39k • written 7.3 years ago by ★ 1.1k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 12 weeks ago by 39k • written 6.8 years ago by 26k
99
votes
21
replies
8.0k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 3 months ago by 39k • written 10.4 years ago by ▴ 370
98
votes
41
replies
4.6k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 8 weeks ago by 39k • written 6.8 years ago by ▴ 510
97
votes
19
replies
89k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 10 months ago by 39k • written 13.3 years ago by 27k
95
votes
27
replies
77k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 20 days ago by • 0 • written 11.0 years ago by ▴ 820
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 3 months ago by 39k • written 10.7 years ago by 98k
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 3 months ago by 39k • written 9.5 years ago by 98k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 12 weeks ago by 39k • written 4.8 years ago by 85k
92
votes
46
replies
10k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 3 months ago by 39k • written 11.9 years ago by 3.2k
92
votes
39
replies
134k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 weeks ago by ▴ 120 • written 10.9 years ago by ▴ 370
91
votes
18
replies
60k
views
12 follow
Sequence length from Fasta
fasta
updated 5 months ago by 39k • written 8.6 years ago by ▴ 80
91
votes
25
replies
58k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 9 months ago by 52k • written 12.3 years ago by 3.4k
91
votes
20
replies
19k
views
15 follow
Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one WGS RNA-Seq next-gen Exome
updated 8 months ago by 39k • written 9.1 years ago by 20k
89
votes
16
replies
20k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat batch-effect sva
updated 4 months ago by ▴ 20 • written 8.0 years ago by ★ 3.0k
89
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 3 months ago by 39k • written 9.6 years ago by 20k
89
votes
31
replies
12k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs visualization genomics
updated 10 months ago by 39k • written 11.3 years ago by ★ 1.5k
1,000 results • Page 2 of 20
Recent Votes
Comment: UCSC genome browser
Answer: Downloading "dbsnp 146.hg38.vcf.gz" file for BQSR
Downloading "dbsnp 146.hg38.vcf.gz" file for BQSR
Answer: Creating a local version of Clustered NR database
Comment: Filtering genes after TPM normalization
Comment: ChatGPT optimized for bioinformatics questions
Answer: Reorder GO terms using R
Recent Locations • All
Philippines, just now
India, 1 minute ago
India, 4 minutes ago
South Korea, 5 minutes ago
Australia, 8 minutes ago
United States, 9 minutes ago
United States, 12 minutes ago
Recent Awards • All
Popular Question to sgujja ▴ 40
Popular Question to asalimih ▴ 60
Popular Question to pehenriquejp • 0
Teacher to Mensur Dlakic ★ 23k
Commentator to GenoMax 130k
Popular Question to Amr ▴ 140
Popular Question to ManuelDB ▴ 40
Recent Replies
Comment: Mapping a predicted sequence to a genome by Mensur Dlakic ★ 23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome by Andy • 0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome by Mensur Dlakic ★ 23k
If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
Comment: How to get information about promoter from bulk-RNAseq? by rfran010 ▴ 170
I'll just add what I did with my own dataset of ribo depleted RNA-seq: I took predicted enhancer-promoter interaction datasets from UCSC a…
Answer: How to get information about promoter from bulk-RNAseq? by rfran010 ▴ 170
What type of RNA-seq data do you have? With polyA, I think it will be hard to incorporate enhancer info without additional datasets. …
Comment: Reorder GO terms using R by hellokwmin • 0
Thank you so much. It worked perfectly.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Thank you so much, Gordon!
Comment: Help with running ATAC using Encode pipeline by rfran010 ▴ 170
Yes, it is a lot to take in. In your input json, is "atac.fastqs_wt_rep2_R2" valid? This key should match exactly what is given in the exa…
Comment: How to calculate TPM from featureCounts output by rfran010 ▴ 170
Yes, I thought the featureCounts file is your counts file.
Comment: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
The code should be: ``` library(edgeR) group<- factor(type) design <- model.matrix(~group) mrna.dge <- DGEList(counts=mat, group=group) ke…
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil by javiflaja • 0
1) I realised I was supposed to add RGs during alingment command only after I was long done with that step. But I imgined the tool "addorre…
Comment: Creating a local version of Clustered NR database by PeterC_NCBI ▴ 260
Thanks @genomax > This seems reasonable since it should capture significant part of sequence to search against ( 90% identity and 90% …
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil by Pierre Lindenbaum 154k
1) read groups should have been specified from the start (eg. with bwa mem -R ) 2) if you do'nt specify SORT_ORDER, the order is the same …
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 100
Does it support substitution matrices - e.g. blossum62 - for local protein alignments ? Does it support different gaps for gat open, and …
Comment: ChatGPT optimized for bioinformatics questions by Alexander ▴ 100
May be you can consider to make a talk about that work for your community "sciBerloga" - see previous talks: https://www.youtube.com/@SciBe…
Traffic: 1426 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6