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1,000 results • Page 4 of 20
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68
votes
48
replies
7.1k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 24 days ago by 39k • written 5.9 years ago by 98k
67
votes
15
replies
32k
views
14 follow
Rna-Seq Pipeline
pipeline next-gen-sequencing rna rna-seq
updated 19 days ago by 39k • written 13.1 years ago by 24k
67
votes
18
replies
70k
views
17 follow
Project For A Beginner Bioinformatics Student
project java
updated 10 months ago by 39k • written 11.6 years ago by ▴ 230
67
votes
21
replies
5.2k
views
8 follow
Forum: Meta: Markdown in Biostars (now enabled)
meta
11 weeks ago by Ram 39k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
66
votes
19
replies
47k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq tools
updated 6 days ago by ▴ 10 • written 10.3 years ago by ★ 3.6k
66
votes
21
replies
5.8k
views
18 follow
Forum: Is there anyone who was a pure biologist?
next-gen
updated 3 months ago by 39k • written 9.1 years ago by ▴ 100
66
votes
6
replies
24k
views
8 follow
What Is A "Spot" In Sra Format
sra fastq format
updated 4 months ago by 39k • written 11.7 years ago by 4.1k
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 3 months ago by 39k • written 9.9 years ago by ★ 3.0k
65
votes
27
replies
6.4k
views
14 follow
Forum: What is the reason for most software errors in Bioinformatics according to you?
software-error blast sequencing SNP R
updated 8 weeks ago by 39k • written 7.2 years ago by ▴ 110
65
votes
35
replies
19k
views
17 follow
Which Dna Compression Algorithms Are Actually Used?
dna
updated 9 months ago by 154k • written 12.0 years ago by ▴ 270
65
votes
17
replies
32k
views
12 follow
Transform a GTF file into a data frame in R
R RNA-Seq GTF
updated 3 months ago by 39k • written 5.7 years ago by ▴ 360
65
votes
3
replies
274k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 3 months ago by 39k • written 9.0 years ago by ▴ 960
65
votes
26
replies
18k
views
13 follow
Forum: Macosx For Bioinformatics?
linux
updated 3 months ago by 39k • written 9.5 years ago by 11k
65
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 12 weeks ago by 39k • written 4.3 years ago by 16k
64
votes
24
replies
2.3k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 11 days ago by 39k • written 4.7 years ago by ▴ 80
64
votes
8
replies
7.8k
views
7 follow
Forum: Isaac Asimov Accurately Predicts Woes Of Bioinformatician
bioinformatician
updated 3 months ago by 39k • written 10.1 years ago by 20k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 11 weeks ago by 39k • written 5.7 years ago by 85k
64
votes
29
replies
14k
views
15 follow
Forum: Fundamentals Of Designing Biological Databases?
database
updated 3 months ago by 39k • written 12.6 years ago by ▴ 130
64
votes
5
replies
6.8k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 7 months ago by 39k • written 7.8 years ago by 12k
63
votes
9
replies
97k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression RNA-Seq
updated 3 months ago by 39k • written 5.7 years ago by ★ 2.1k
63
votes
27
replies
26k
views
18 follow
Data Too Big To Be Stored In Memory: Common Options
python
updated 3 months ago by 39k • written 10.5 years ago by ▴ 720
63
votes
19
replies
20k
views
12 follow
What Ngs Read Simulators Are Available For Paired-End Data?
next-gen sequencing fastq simulation paired
updated 7 months ago by 39k • written 12.8 years ago by 12k
63
votes
28
replies
3.2k
views
11 follow
Forum: Bioinformatics analyses & errors: need for better post-publication tools?
next-gen RNA-Seq
updated 8 weeks ago by 39k • written 7.1 years ago by ★ 1.2k
63
votes
9
replies
3.6k
views
Forum: Should The "Post Closing" Option Exist? Vote Now!
meta
updated 3 months ago by 39k • written 10.0 years ago by 98k
62
votes
14
replies
186k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 6 weeks ago by 11k • written 10.3 years ago by ▴ 900
62
votes
22
replies
57k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 5 months ago by • 0 • written 10.6 years ago by ★ 1.5k
62
votes
16
replies
32k
views
18 follow
Job: Bioinformatics Jobs You Can Do From Home?
python education
updated 3 months ago by 39k • written 12.7 years ago by ▴ 290
62
votes
24
replies
39k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 5 months ago by 39k • written 9.0 years ago by ▴ 170
61
votes
14
replies
19k
views
13 follow
Why is Hadoop not used a lot in bio-informatics?
hadoop
updated 12 weeks ago by 39k • written 8.7 years ago by ★ 5.2k
61
votes
11
replies
14k
views
9 follow
Forum: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
programming
updated 3 months ago by 39k • written 9.9 years ago by 19k
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 3 months ago by 39k • written 9.2 years ago by 98k
61
votes
16
replies
6.5k
views
14 follow
Forum: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
library
updated 4 months ago by ★ 1.3k • written 2.6 years ago by 8.1k
61
votes
29
replies
6.5k
views
14 follow
Best bioinfo one-liners?
linux
updated 5 months ago by 39k • written 8.1 years ago by 4.1k
60
votes
6
replies
9.0k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 3 months ago by 39k • written 9.8 years ago by 9.6k
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
60
votes
3
replies
32k
views
Paired-end reads - what is what?
RNA-Seq
updated 5 months ago by 39k • written 8.0 years ago by ▴ 220
60
votes
2
replies
7.0k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
60
votes
17
replies
31k
views
16 follow
Scientific Names In Blast Output And Databases
blast blast+
updated 5 months ago by 39k • written 9.9 years ago by ★ 2.0k
60
votes
18
replies
3.3k
views
10 follow
Are Super User Style Questions Appropriate In Biostar?
meta biostars
updated 3 months ago by 39k • written 12.9 years ago by ▴ 460
60
votes
14
replies
11k
views
14 follow
Forum: Interesting bioinformatics blogs (2017 edition)
blogs
updated 3 months ago by 39k • written 6.2 years ago by 47k
60
votes
17
replies
31k
views
7 follow
how to remove multiallelic from VCF
SNP
updated 3 months ago by 39k • written 8.1 years ago by ▴ 510
60
votes
12
replies
35k
views
10 follow
Get chromosome sizes from fasta file
genome ucsc
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 700
60
votes
28
replies
7.3k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 12 weeks ago by 39k • written 8.7 years ago by 98k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 11 days ago by 39k • written 4.7 years ago by 16k
59
votes
95
replies
15k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 4 months ago by ▴ 10 • written 5.1 years ago by ▴ 260
59
votes
36
replies
35k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 10 months ago by ▴ 40 • written 11.1 years ago by ▴ 820
59
votes
31
replies
3.7k
views
12 follow
News: Example of how bioinformaticians can publish in Scientific Reports (by nature publishing group) using publicly available NGS data
publication NGS
updated 7 weeks ago by 39k • written 6.4 years ago by 9.9k
59
votes
43
replies
19k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 11 weeks ago by 39k • written 5.7 years ago by ★ 1.4k
58
votes
19
replies
20k
views
11 follow
Current state-of-the-art for RNA-Seq gene / transcript expression quantification OR just the tools of preference
kallisto salmon bitseq RNA-Seq cufflinks
updated 8 months ago by 39k • written 7.7 years ago by ★ 1.3k
1,000 results • Page 4 of 20
Recent Votes
Answer: Gene enrichment analysis
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
Comment: Getting Pairwise Sequence Alignment Score With Biopython
C: How does salmon deal with decoy?
A: How does salmon deal with decoy?
A: How does salmon deal with decoy?
Comment: Italicise annotations with pheatmap
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Popular Question to Chris ▴ 100
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Recent Replies
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Sure, here is my json file, I have 8 fastq files: { "atac.title" : “atac)”, "atac.description" : “Encode”, …
Comment: Differential protein expression analysis by dsull ★ 4.2k
Yes, you need to log-transform. I've had a good experience using limma for proteomics analyses (limma uses a moderated t-test).
Answer: Assigned taxonomy after dada2 only "NAs" or "Mitochondria" by mattze731 ▴ 10
Never mind. Someone had put all the 16S files into the ITS folder and vice versa. After using the 16S dada2 pipeline on the actual 16S file…
Comment: Getting Pairwise Sequence Alignment Score With Biopython by Jonathan Lefebre ▴ 70
Dear Alexander, to answer 2) first: This is just a fasta file that you can obtain essentially from every multiple sequence alignment soft…
Comment: Stratified sample assignment for analysis by ATpoint 72k
Batches for what? Processing/sequencing, what data are we talking about? If this is indeed paired then you basically must keep samples of a…
Answer: Visualizing Graph Alignment Format via minigraph by colindaven 4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin by i.sudbery 17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin by i.sudbery 17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis by Vincent Laufer ★ 2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq. Generally, your options …
Comment: VEP tab/vcf - Different output by Ben_Ensembl ★ 2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms by Alexander ▴ 70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython by Alexander ▴ 70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments. I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use? by fracarb8 ▴ 950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software by alexandru.bologa.marian ▴ 40
Hi, I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython by Jonathan Lefebre ▴ 70
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
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