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118,801 results • Page 5 of 2377
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81
votes
22
replies
94k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen sequencing fasta rna r perl
updated 22 months ago by 44k • written 12.9 years ago by ▴ 290
81
votes
4
replies
21k
views
Discrimination Between Germline And Somatic Mutations In Tumor Without The Availability Of The Normal Paired Sample
mutation somatic
updated 11.6 years ago by 4.4k • written 11.6 years ago by 4.3k
81
votes
23
replies
13k
views
10 follow
Transform A Pipeline Of R Scripts Into A Web Application
webservice web pipeline galaxy
updated 2.4 years ago by 44k • written 14.1 years ago by 28k
81
votes
6
replies
47k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 2.5 years ago by 44k • written 12.4 years ago by 4.4k
81
votes
21
replies
5.4k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 18 months ago by 44k • written 8.3 years ago by ★ 3.2k
81
votes
15
replies
24k
views
10 follow
Vertebrate Subset Nr Database? Build My Own?
blast database
updated 10.3 years ago by • 0 • written 13.5 years ago by ▴ 430
81
votes
39
replies
8.1k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 19 months ago by 44k • written 11.7 years ago by 101k
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 10 months ago by 44k • written 14.5 years ago by 13k
81
votes
21
replies
44k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 12 months ago by ▴ 210 • written 10.6 years ago by ▴ 750
80
votes
21
replies
39k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 10 months ago by • 0 • written 10.4 years ago by ▴ 660
80
votes
34
replies
5.7k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 20 months ago by 44k • written 9.3 years ago by ▴ 520
80
votes
27
replies
58k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 2.1 years ago by ▴ 70 • written 10.8 years ago by ▴ 190
80
votes
23
replies
5.7k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 18 months ago by 44k • written 9.9 years ago by ★ 3.0k
80
votes
16
replies
51k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation academic style
updated 8.4 years ago by 24k • written 8.5 years ago by ★ 1.1k
80
votes
24
replies
12k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 10 months ago by 44k • written 14.4 years ago by 28k
79
votes
24
replies
63k
views
16 follow
How To Sort Bed Format File
bed
updated 23 months ago by 163k • written 11.6 years ago by ▴ 470
79
votes
38
replies
36k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 6 months ago by ▴ 60 • written 8.2 years ago by 6.6k
79
votes
10
replies
23k
views
6 follow
what do the headers of the rMATS output files mean?
MATS Alternative splicing next-gen STAR
updated 5.9 years ago by • 0 • written 7.3 years ago by ▴ 140
79
votes
35
replies
10k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 16 months ago by • 0 • written 8.8 years ago by ▴ 650
79
votes
86
replies
34k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 15 months ago by 44k • written 7.8 years ago by 20k
78
votes
26
replies
127k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 10 months ago by ★ 2.8k • written 9.4 years ago by ▴ 260
78
votes
22
replies
23k
views
14 follow
Assessing The Quality Of De Novo Assembled Data
assembly next-gen
updated 24 months ago by 44k • written 12.3 years ago by ★ 2.7k
78
votes
12
replies
40k
views
8 follow
How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19
position ucsc
updated 5.9 years ago by ▴ 100 • written 14.1 years ago by ▴ 260
78
votes
31
replies
7.2k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 19 months ago by 44k • written 13.6 years ago by 10k
77
votes
9
replies
13k
views
15 follow
Which program, tool, or strategy do you use to visualize genomic rearrangements?
fusion-genes visualizations rearrangements
updated 2.0 years ago by 44k • written 9.0 years ago by ★ 1.1k
77
votes
13
replies
16k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.9 years ago by 44k • written 10.3 years ago by 20k
77
votes
15
replies
11k
views
10 follow
Best Bioinformatics Research Images
visualization
updated 13.2 years ago by 7.4k • written 13.3 years ago by 2.3k
77
votes
20
replies
15k
views
12 follow
Perl Or Python For Comparative Genomics?
bioperl biopython python comparative
updated 6.3 years ago by 5.8k • written 14.0 years ago by ★ 2.0k
77
votes
16
replies
35k
views
14 follow
Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier
genbank conversion ncbi taxonomy
updated 7.6 years ago by ★ 1.1k • written 13.1 years ago by ▴ 490
77
votes
11
replies
33k
views
9 follow
Star Or Tophat?
rnaseq alignment tophat
updated 3.4 years ago by 44k • written 10.7 years ago by ▴ 970
77
votes
18
replies
47k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 2.1 years ago by • 0 • written 14.3 years ago by ★ 1.1k
76
votes
72
replies
21k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
4 months ago by Kevin Blighe 88k
76
votes
14
replies
13k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 15 months ago by 44k • written 7.3 years ago by ★ 3.4k
76
votes
14
replies
17k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 19 months ago by 44k • written 11.3 years ago by 9.8k
76
votes
22
replies
56k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 18 months ago by 44k • written 10.6 years ago by ★ 1.5k
76
votes
24
replies
21k
views
18 follow
What Methods Do You Use For Short Read Mapping?
short-read-aligner sequence
updated 5.1 years ago by 44k • written 14.6 years ago by ★ 1.0k
75
votes
60
replies
29k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 19 months ago by 44k • written 7.0 years ago by 88k
75
votes
13
replies
67k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
classification r cancer randomForest machine-learning
updated 7 weeks ago by 20k • written 10.8 years ago by ★ 1.2k
75
votes
3
replies
40k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.8 years ago by 44k • written 10.2 years ago by 101k
75
votes
19
replies
4.1k
views
11 follow
Blog: A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 6 months ago by 4.4k • written 12 months ago by ▴ 30
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 10 months ago by 44k • written 14.4 years ago by 163k
75
votes
27
replies
29k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by • 0 • written 10.6 years ago by 101k
74
votes
14
replies
30k
views
12 follow
Forum: Bioinformatics Consulting Thoughts
consulting
updated 2.2 years ago by 44k • written 14.3 years ago by 4.6k
74
votes
16
replies
5.1k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
subjective
updated 14 months ago by 44k • written 13.5 years ago by ★ 3.3k
74
votes
15
replies
52k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
written 6.4 years ago by ▴ 420
73
votes
14
replies
4.6k
views
12 follow
Forum: Things you wish you knew when entering the bioinformatics field
pitfalls advice
updated 15 months ago by 44k • written 4.0 years ago by ★ 17k
73
votes
7
replies
13k
views
6 follow
What Should I Use Blat For?
alignment
updated 11.8 years ago by 11k • written 11.8 years ago by ★ 4.1k
73
votes
16
replies
92k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 2.5 years ago by 163k • written 13.0 years ago by ▴ 530
73
votes
25
replies
9.3k
views
16 follow
The Five Most Annoying Bioinformatics Problems You Face Every Week?
updated 11.0 years ago by 11k • written 11.0 years ago by ▴ 60
72
votes
18
replies
7.8k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 19 months ago by 44k • written 11.2 years ago by 8.7k
118,801 results • Page 5 of 2377
Recent Votes
Assistant, Associate, or Full Project Scientist in Cell & Developmental Biology UC San Diego
Answer: Hugely different results between edgeR and DESeq2
Comment: homer motif search
Comment: Snakemake-Created Conda Environment Deactivation
Answer: multiple sequence alignmet
Comment: Snakemake-Created Conda Environment Deactivation
Comment: multiple sequence alignmet
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Recent Replies
Answer: Integration of paired and single-end SRA by Brian Bushnell 20k
I don't know how GATK will react, but in principle there's no problem. For BBTools, at least, more coverage is always better when doing va…
Answer: High inconsistency between edgeR and DESeq2 by bk11 ★ 2.9k
Please check the post here. It has been discussed very explicitly before. [https://www.biostars.org/p/9552174/][1] [1]: https://…
Comment: Find all sequences with adapters without trimming them off by Brian Bushnell 20k
Actually, I forgot to add the flag "rcomp=f"; the command I gave will also match "CANNNNAC" which is probably why the number is a little hi…
Comment: New Illumina error mode, new BBTools release (39.09) to deal with it by Brian Bushnell 20k
You can run BBCMS to clean up the reads a bit prior to assembly... we do that for all of our big metagenomes. Something like: bbcms.sh i…
Comment: Snakemake-Created Conda Environment Deactivation by hugo.avila ▴ 530
Yeah, very good points. This is not normal behavior at all. Once, I had some trouble with environments on a Slurm node, but nothing like t…
Comment: Salmon quantification not as expected; "versionInfo.json doesn't seem to exist" by Haad • 0
Ah yeah I think it's likely that there was no space to make those files. The program did run because just for testing purposes I had a prin…
Comment: Best practice for gene ontology/pathway/geneset enrichment in 10x data by jared.andrews07 ★ 17k
Having recently done something similar, I found it easier to integrate samples prior to clustering/annotating or doing DE. But it really de…
Comment: Best practice for gene ontology/pathway/geneset enrichment in 10x data by jared.andrews07 ★ 17k
Pseudobulk is definitely the way to go, FindAllMarkers is just not very robust in my opinion, and the bulk methods work well when counts ar…
Comment: Different result by bowtie2 by dthorbur ★ 2.4k
There are many reasons you might get different number of reads with a tool like `Bowtie2`. The tool uses heuristics to be fast and efficien…
Answer: Snakemake - Missing output files by tim.booth ▴ 90
For any **vim** users reading this, add this to your *.vimrc*: ``` highlight default ExtraWhitespace ctermbg=darkgreen guibg=#216000 m…
Comment: Snakemake-Created Conda Environment Deactivation by tim.booth ▴ 90
It's even weirder than that. Snakemake is a Python program so it runs as a child process spawned by the shell, then when Snakemake runs any…
Comment: Best practice for gene ontology/pathway/geneset enrichment in 10x data by yura.grabovska ▴ 430
I'm currently running pseudo-bulk using the relevant section of the [Seurat vignette](https://satijalab.org/seurat/articles/de_vignette) to…
Comment: Best practice for gene ontology/pathway/geneset enrichment in 10x data by yura.grabovska ▴ 430
The dataset is cells treated with a drug across 3 timepoints. Each timepoint has 3 replicates. Using AddModuleScore() for signatures of int…
Answer: Best practice for gene ontology/pathway/geneset enrichment in 10x data by bk11 ★ 2.9k
You may consider using pseudo-bulk analysis approach with gene set tests implemented in `limma` if your datasets have a complex experimenta…
Comment: Best practice for gene ontology/pathway/geneset enrichment in 10x data by jared.andrews07 ★ 17k
What is your goal? Are you certain the clusters actually represent distinct cell types or states? How many genes are you getting out from m…
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