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110,351 results • Page 1 of 2208
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Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 months ago by ▴ 250 • written 12.2 years ago by 21k
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 days ago by 39k • written 7.8 years ago by ★ 4.6k
743
votes
162
replies
113k
views
101 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 4 weeks ago by 1.8k • written 6.5 years ago by 98k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
298
votes
121
replies
26k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 4 months ago by ▴ 250 • written 12.9 years ago by 11k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 weeks ago by 39k • written 4.7 years ago by 85k
59
votes
95
replies
15k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 3 months ago by ▴ 10 • written 5.1 years ago by ▴ 260
323
votes
90
replies
218k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 8 months ago by 39k • written 12.3 years ago by 4.9k
76
votes
86
replies
26k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 5 months ago by 129k • written 6.5 years ago by 18k
128
votes
83
replies
10k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
fastq compressor lossless fastq compression Tool
5.8 years ago by Petr Ponomarenko ★ 2.7k
360
votes
81
replies
137k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
5 weeks ago by ole.tange ★ 4.3k
102
votes
81
replies
25k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 9 months ago by 129k • written 6.4 years ago by ★ 1.9k
117
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 7 months ago by 129k • written 12.5 years ago by ★ 3.3k
56
votes
72
replies
4.0k
views
8 follow
Dear biostars I really need your kindly help, please save me from this hardship situation
software error mirddep2 perl miRNAs RNA-Seq
updated 6.6 years ago by ▴ 100 • written 6.7 years ago by ★ 4.2k
105
votes
72
replies
14k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 4.7 years ago by 11k • written 12.9 years ago by 11k
71
votes
71
replies
25k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot ggplot2 ggrepel bioconductor Tool
updated 7 months ago by ▴ 40 • written 4.7 years ago by 85k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 11 weeks ago by 39k • written 5.3 years ago by 85k
164
votes
70
replies
56k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.4 years ago by ▴ 430 • written 11.9 years ago by ★ 1.8k
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 3 months ago by 39k • written 9.1 years ago by 98k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 8 weeks ago by ▴ 10 • written 5.5 years ago by 85k
279
votes
69
replies
18k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 3 months ago by 39k • written 11.8 years ago by ▴ 160
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 11 weeks ago by 39k • written 4.9 years ago by 72k
134
votes
65
replies
3.9k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 16 months ago by 52k • written 3.5 years ago by ▴ 880
306
votes
65
replies
20k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 8 months ago by 85k • written 13.3 years ago by 27k
286
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 8 months ago by 85k • written 12.2 years ago by 22k
160
votes
63
replies
76k
views
38 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 4 hours ago by ▴ 30 • written 12.2 years ago by 4.1k
38
votes
63
replies
17k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 3 months ago by 39k • written 10.3 years ago by 4.2k
144
votes
62
replies
9.6k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 3 months ago by 39k • written 12.2 years ago by ★ 2.9k
34
votes
62
replies
4.4k
views
6 follow
Extract some features from a combined gene bank file in bash
gene sequence genome gene bank NCBI
updated 6.6 years ago by 39k • written 6.6 years ago by ★ 4.2k
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
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 3 months ago by 39k • written 8.1 years ago by ▴ 30
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
65
votes
57
replies
6.3k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 15 months ago by 39k • written 8.6 years ago by ▴ 20
361
votes
57
replies
61k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 8 months ago by 85k • written 13.2 years ago by 98k
26
votes
57
replies
6.3k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 2.4 years ago by 39k • written 4.6 years ago by ▴ 510
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
145
votes
56
replies
7.5k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 3 months ago by 39k • written 10.2 years ago by 98k
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 3 months ago by 39k • written 10.1 years ago by 9.6k
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.2 years ago by midox ▴ 290
46
votes
54
replies
5.1k
views
12 follow
fasta seq header
sequence fasta
updated 6.2 years ago by 10k • written 6.3 years ago by ▴ 220
328
votes
54
replies
58k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 8 months ago by 85k • written 13.2 years ago by 24k
55
votes
53
replies
4.7k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria kraken spades blast sendsketch
updated 3.5 years ago by ▴ 30 • written 3.7 years ago by ▴ 200
6
votes
53
replies
2.6k
views
how to download all sequences from web link
bash linux
3.9 years ago by Bioinfonext ▴ 430
113
votes
53
replies
5.2k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 18 hours ago by 39k • written 4.1 years ago by ▴ 170
120
votes
53
replies
90k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 10 weeks ago by • 0 • written 9.0 years ago by ▴ 330
54
votes
52
replies
45k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Tool on Gene Clustering Function based
updated 17 months ago by 39k • written 8.8 years ago by 7.5k
85
votes
52
replies
8.5k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 2.5 years ago by ▴ 130 • written 13.2 years ago by 3.4k
88
votes
52
replies
46k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 18 months ago by ▴ 10 • written 5.6 years ago by ▴ 210
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 3.3k
160
votes
52
replies
119k
views
28 follow
Fastq Convert To Fasta
perl
9.6 years ago by biolab ★ 1.4k
110,351 results • Page 1 of 2208
Recent Votes
Answer: Alignment of case vs. control from different origin
What type of normalization did they use in this article?
Answer: I don't want to believe the Interproscan DB estimated download time.
C: removing overrepresented sequences from rna-seq
C: removing overrepresented sequences from rna-seq
C: Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Answer: Any methods available to do QC analysis of Pacbio raw data??
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Recent Replies
Comment: What type of normalization did they use in this article? by JACKY ▴ 90
I see, do you think there is any way to retrieve the uncorrected TPM data? can I undo the corrections and scalings applied to the data?
Comment: Alignment of case vs. control from different origin by ATpoint 72k
I would not even do the trimming. Any differential analysis of case (normal/control) versus anything in TCGA (progressed cancer) is going t…
Comment: Docker Error while running nf-core/rnaseq pipeline by eesha28112001 • 0
How do I do that?
Comment: MACS2 peak calling by ATpoint 72k
You do not need strand information for this as, as I said, strands do not apply in DNA-seq.
Answer: Docker Error while running nf-core/rnaseq pipeline by ATpoint 72k
> read-only file system You must make sure that the output destination is writable.
Answer: sctransform on scRNA seq by ATpoint 72k
No, there is no magic to make data appear where previously there were none.
Answer: What type of normalization did they use in this article? by Matthias Zepper 3.7k
> Transcriptomic analysis > > [...] We subsequently filtered genes that > were not expressed in any of the samples (in each cohort > indep…
Comment: How to get a comperative result of 2 bed files? by Pierre Lindenbaum 154k
what kind of measurement do you need ? I see one bed file in your description , what are the TWO bed file ?
Comment: MACS2 peak calling by Maurice • 0
Thank you! And for what regards peaks annotation, how can the tool I'm going to use assign peaks to the correct location without knowing t…
Comment: sorting BAM file by ATpoint 72k
You can simply use `samtools sort` to get rid of this read group nonsense these Broad institute tools always complain about.
Answer: Which type of variant caller should I use in a WES normal cell line sample? by ATpoint 72k
Any variant caller will do. Somatic calling is usually an additional mode while calling without matched normal is typically always possible.
Comment: Create customized gene annotation file by ATpoint 72k
Plese confirm whether you read and tried the manual: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/…
Answer: MACS2 peak calling by ATpoint 72k
Yes, that is correct. Peaks from experiments such as ChIP-seq or ATAC-seq are based on DNA, which is double-stranded and unlike RNA (where …
Answer: Alignment of case vs. control from different origin by i.sudbery 17k
I hate to be the one to tell you this, but the reason you have been unable to find an answer isnthat what you are trying to do is not gener…
Answer: Peaks annotation on bacterial genome by Maurice • 0
Thank you for your kind reply! I have just a further question. Which is the difference between using annoPeaks and annotatePeaksinbatch wi…
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