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1,000 results • Page 8 of 20
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61
votes
21
replies
12k
views
13 follow
Where Would You Host Your Open Source Code Repository Today?
updated 10.8 years ago by ▴ 80 • written 13.1 years ago by ▴ 220
61
votes
70
replies
14k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 15 months ago by 43k • written 10.1 years ago by 100k
61
votes
14
replies
11k
views
11 follow
Recommend Easy To Use Microarray Clustering Software
microarray clustering
updated 7 months ago by 43k • written 14.6 years ago by 100k
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 5 months ago by ★ 1.2k • written 11.2 years ago by ★ 1.3k
61
votes
27
replies
27k
views
18 follow
Links To Good Next Gen Sequence Analysis Training Courses And Centres
next-gen sequencing analysis workshops training
updated 2.1 years ago by 43k • written 12.8 years ago by ★ 2.8k
60
votes
18
replies
10k
views
12 follow
Figure Of Diminishing Sequencing Costs
next-gen sequencing cost
updated 9.4 years ago by 20k • written 13.5 years ago by 11k
60
votes
21
replies
14k
views
15 follow
Which Is The Best Software To Represent Biological Pathways In A Directed Graph (Network) ?
kegg pathway network
updated 9.7 years ago by ▴ 350 • written 13.7 years ago by ▴ 180
60
votes
18
replies
4.1k
views
10 follow
Are Super User Style Questions Appropriate In Biostar?
meta biostars
updated 15 months ago by 43k • written 13.8 years ago by ▴ 460
60
votes
9
replies
22k
views
7 follow
Getting Allele Frequencies From 1000 Genomes
genome hapmap maf ucsc ensembl
updated 7.2 years ago by ▴ 150 • written 13.1 years ago by 2.8k
60
votes
13
replies
25k
views
13 follow
Any Tools To Identify Significantly Altered Pathways?
pathway kegg microarray
updated 2.4 years ago by 43k • written 13.4 years ago by ★ 1.3k
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general subjective
updated 7 months ago by 43k • written 14.3 years ago by 28k
60
votes
28
replies
8.3k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 14 months ago by 43k • written 9.6 years ago by 100k
60
votes
2
replies
7.4k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
60
votes
52
replies
44k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 14 months ago by 43k • written 7.6 years ago by ★ 3.5k
60
votes
6
replies
27k
views
What is the difference between a Read and a Fragment in RNA-seq?
rna-seq sequencing fragment read insert
updated 2.5 years ago by 43k • written 9.8 years ago by ▴ 660
60
votes
12
replies
4.7k
views
11 follow
Database Of Databases?
database online
updated 7.1 years ago by ▴ 50 • written 13.1 years ago by ▴ 230
60
votes
9
replies
36k
views
7 follow
How To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific
illumina paired-end strand trinity
updated 3.5 years ago by • 0 • written 11.2 years ago by ▴ 190
60
votes
12
replies
42k
views
10 follow
Get chromosome sizes from fasta file
genome ucsc
updated 18 months ago by • 0 • written 8.3 years ago by ▴ 710
60
votes
15
replies
78k
views
9 follow
BAM/SAM to FASTA conversion
sam bam
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.4k
60
votes
15
replies
50k
views
11 follow
Estimate Insert Size In Paired-End/Mate-Pair
next-gen sequencing alignment paired
updated 2.5 years ago by 43k • written 12.3 years ago by ▴ 190
60
votes
17
replies
35k
views
16 follow
Scientific Names In Blast Output And Databases
blast blast+
updated 16 months ago by 43k • written 10.8 years ago by ★ 2.1k
60
votes
21
replies
3.9k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome assembly
updated 8 months ago by 54k • written 8 months ago by ▴ 60
60
votes
25
replies
5.7k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size statistical-power RNA-Seq
updated 11 months ago by 43k • written 3.7 years ago by ▴ 230
60
votes
14
replies
12k
views
16 follow
Forum: Interesting bioinformatics blogs (2017 edition)
blogs
updated 14 months ago by 43k • written 7.1 years ago by 47k
59
votes
36
replies
39k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 21 months ago by ▴ 40 • written 12.0 years ago by ▴ 830
59
votes
31
replies
5.0k
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 13 months ago by 43k • written 7.4 years ago by 11k
59
votes
43
replies
21k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 14 months ago by 43k • written 6.7 years ago by ★ 1.4k
59
votes
12
replies
16k
views
10 follow
Transcription Factor Binding Sites Database For Bacteria?
transcription binding bacteria
updated 5.7 years ago by ▴ 20 • written 13.2 years ago by ▴ 230
59
votes
25
replies
25k
views
12 follow
How To Map A Snp To A Gene Around +/- 60Kb ?
snp data human annotation
updated 14.2 years ago by 12k • written 14.2 years ago by 18k
59
votes
15
replies
38k
views
13 follow
Retrieve All Genes Associated With A Go Term
r bioconductor go gene-ontology
updated 2.1 years ago by 82k • written 11.7 years ago by ▴ 900
59
votes
23
replies
6.2k
views
16 follow
What Do Bioinformaticians Use To Make High Quality Web Sites?
web
updated 13.2 years ago by ★ 2.5k • written 13.2 years ago by ▴ 980
58
votes
10
replies
6.8k
views
7 follow
Rationale For Pca Analysis
pca feature
updated 13.2 years ago by • 0 • written 13.2 years ago by ▴ 280
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 6 months ago by 43k • written 14.1 years ago by 18k
58
votes
26
replies
22k
views
13 follow
single line fasta to mult line fasta
fasta
updated 6.3 years ago by • 0 • written 7.8 years ago by ▴ 20
58
votes
15
replies
4.3k
views
11 follow
What Is Your Favorite Wiki Use Case In Bioinformatics?
papers
updated 13.3 years ago by 3.2k • written 13.6 years ago by 5.4k
58
votes
22
replies
15k
views
15 follow
Huge Ngs Data Storage And Transferring
next-gen sequencing fastq
updated 10.4 years ago by ★ 1.3k • written 13.2 years ago by ▴ 90
58
votes
8
replies
27k
views
7 follow
Duplicated Reads In Rna-Seq Experiment
rna duplicates
updated 12.5 years ago by 20k • written 12.5 years ago by ▴ 580
58
votes
8
replies
8.4k
views
8 follow
What is the best way to combine machine learning algorithms for feature selection such as Variable importance in Random Forest with differential expr…
RNA-Seq rna-seq
updated 7 months ago by • 0 • written 6.1 years ago by ▴ 150
58
votes
19
replies
21k
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 20 months ago by 43k • written 8.7 years ago by ★ 1.3k
58
votes
25
replies
40k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 14 months ago by 43k • written 7.8 years ago by ★ 9.4k
57
votes
24
replies
6.5k
views
14 follow
News: Join us in building a bioinformatics resource: The Biostar Handbook
biostar-handbook
updated 20 months ago by 43k • written 8.7 years ago by 100k
57
votes
23
replies
16k
views
9 follow
Any Good Bed/Wig Parsers In Python ?
python parsing bed wiggle
updated 8.0 years ago by 20 • written 13.1 years ago by ▴ 120
57
votes
42
replies
6.7k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 2.3 years ago by 43k • written 9.6 years ago by 33k
57
votes
15
replies
20k
views
14 follow
Bioinformatics And Computer Science
updated 3.2 years ago by ▴ 50 • written 13.8 years ago by ▴ 80
57
votes
23
replies
46k
views
14 follow
Bam File: Change Chromosome Notation
samtools bam
updated 3.0 years ago by 11k • written 12.6 years ago by ▴ 160
57
votes
19
replies
28k
views
6 follow
Forum: Attention: Bowtie2 And Multiple Hits
next-gen bowtie mapping
updated 14 months ago by 43k • written 11.6 years ago by 11k
57
votes
35
replies
15k
views
9 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP genotype GATK
updated 7 months ago by 88k • written 6.3 years ago by ▴ 520
57
votes
15
replies
6.3k
views
9 follow
Forum: Good practices while dealing with very large datasets
Big-Data Programming
updated 12 months ago by 43k • written 7.0 years ago by ★ 1.2k
57
votes
15
replies
4.8k
views
9 follow
Forum: Entice Biologists To Learn R
r
updated 15 months ago by 43k • written 12.6 years ago by 5.3k
57
votes
10
replies
22k
views
6 follow
1000 Genomes Snps' Ancestral Allele
snp 1000genomes
11.3 years ago by seaboy ▴ 130
1,000 results • Page 8 of 20
Recent Votes
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
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Answer: calculating genomic coverage/ base overlap in R by marco.barr ▴ 110
with `findOverlaps` function in `GenomicRanges` package or directly with this package `GeneOverlap`. Check out the documentation of these …
Comment: Annotating file using bcftools by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Annotating file using bcftools by Pierre Lindenbaum 161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
Comment: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
I had the same problem in this iusse [https://github.com/nanoporetech/dorado/issues/603][1] and I solved it as they say here [1]: https…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by ATpoint 82k
Looking at this briefly, it is small sample size and you do not correct for any potential confounders. Use PCA or MDS to explore the data. …
Comment: bbmerge (bbmap) ~ error with insert size file output by GenoMax 142k
> It is confirmed (and solved in another thread) that we have significant overlapping paired end reads. Can you provide a reference to sai…
Comment: Duplicated reads (IDs) from nanopore sequencing by GenoMax 142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data by i.sudbery 19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis by Jacek ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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