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1,000 results • Page 4 of 20
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65
votes
26
replies
19k
views
13 follow
Forum: Macosx For Bioinformatics?
linux
updated 9 months ago by 41k • written 10.0 years ago by 11k
65
votes
27
replies
6.9k
views
14 follow
Forum: What is the reason for most software errors in Bioinformatics according to you?
software-error blast sequencing SNP R
updated 7 months ago by 41k • written 7.7 years ago by ▴ 110
65
votes
10
replies
3.2k
views
6 follow
Incentive For Learning Emboss
emboss
updated 5 months ago by 41k • written 12.6 years ago by 11k
65
votes
3
replies
284k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 8 months ago by 41k • written 9.5 years ago by ▴ 960
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 months ago by 41k • written 4.7 years ago by 16k
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 9 months ago by 41k • written 10.4 years ago by ★ 3.0k
64
votes
24
replies
2.7k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 6 months ago by 41k • written 5.2 years ago by ▴ 80
64
votes
8
replies
8.0k
views
7 follow
Forum: Isaac Asimov Accurately Predicts Woes Of Bioinformatician
bioinformatician
updated 9 months ago by 41k • written 10.6 years ago by 20k
64
votes
29
replies
15k
views
15 follow
Forum: Fundamentals Of Designing Biological Databases?
database
updated 9 months ago by 41k • written 13.1 years ago by ▴ 130
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 months ago by 41k • written 6.2 years ago by 86k
64
votes
9
replies
104k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression RNA-Seq
updated 9 months ago by 41k • written 6.2 years ago by ★ 2.2k
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.1 years ago by 16k
63
votes
11
replies
15k
views
9 follow
Forum: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
programming
updated 9 months ago by 41k • written 10.4 years ago by 19k
63
votes
9
replies
3.8k
views
Forum: Should The "Post Closing" Option Exist? Vote Now!
meta
updated 9 months ago by 41k • written 10.5 years ago by 99k
63
votes
27
replies
26k
views
18 follow
Data Too Big To Be Stored In Memory: Common Options
python
updated 9 months ago by 41k • written 11.0 years ago by ▴ 720
63
votes
28
replies
3.6k
views
11 follow
Forum: Bioinformatics analyses & errors: need for better post-publication tools?
next-gen RNA-Seq
updated 7 months ago by 41k • written 7.6 years ago by ★ 1.2k
62
votes
17
replies
34k
views
7 follow
how to remove multiallelic from VCF
SNP
updated 9 months ago by 41k • written 8.6 years ago by ▴ 530
62
votes
24
replies
41k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 11 months ago by 41k • written 9.5 years ago by ▴ 170
62
votes
14
replies
191k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 7 months ago by 11k • written 10.8 years ago by ▴ 900
62
votes
95
replies
18k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 9 months ago by ▴ 10 • written 5.6 years ago by ▴ 260
62
votes
22
replies
61k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 11 months ago by • 0 • written 11.1 years ago by ★ 1.5k
62
votes
29
replies
7.1k
views
14 follow
Best bioinfo one-liners?
linux
updated 10 months ago by 41k • written 8.5 years ago by 4.1k
62
votes
16
replies
33k
views
18 follow
Job: Bioinformatics Jobs You Can Do From Home?
python education
updated 9 months ago by 41k • written 13.2 years ago by ▴ 290
61
votes
6
replies
9.3k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by 41k • written 10.3 years ago by 9.7k
61
votes
16
replies
7.4k
views
14 follow
Forum: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
library
updated 10 months ago by ★ 1.3k • written 3.1 years ago by 8.3k
61
votes
14
replies
19k
views
13 follow
Why is Hadoop not used a lot in bio-informatics?
hadoop
updated 8 months ago by 41k • written 9.1 years ago by ★ 5.2k
61
votes
14
replies
11k
views
11 follow
Recommend Easy To Use Microarray Clustering Software
microarray clustering
updated 6 weeks ago by 41k • written 14.2 years ago by 99k
61
votes
23
replies
54k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 7 days ago by ★ 1.2k • written 10.8 years ago by ★ 1.3k
61
votes
51
replies
21k
views
9 follow
Tool: Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff sequence fastq next-gen
updated 5 months ago by 41k • written 9.6 years ago by ▴ 790
61
votes
70
replies
13k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 9 months ago by 41k • written 9.6 years ago by 99k
60
votes
14
replies
12k
views
16 follow
Forum: Interesting bioinformatics blogs (2017 edition)
blogs
updated 9 months ago by 41k • written 6.7 years ago by 47k
60
votes
2
replies
7.2k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 9 months ago by 41k • written 11.2 years ago by 99k
60
votes
3
replies
32k
views
Paired-end reads - what is what?
RNA-Seq
updated 10 months ago by 41k • written 8.5 years ago by ▴ 220
60
votes
17
replies
33k
views
16 follow
Scientific Names In Blast Output And Databases
blast blast+
updated 11 months ago by 41k • written 10.4 years ago by ★ 2.1k
60
votes
25
replies
21k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general subjective
updated 6 weeks ago by 41k • written 13.8 years ago by 28k
60
votes
52
replies
42k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.4k
60
votes
18
replies
3.6k
views
10 follow
Are Super User Style Questions Appropriate In Biostar?
meta biostars
updated 9 months ago by 41k • written 13.3 years ago by ▴ 460
60
votes
21
replies
3.3k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome assembly
updated 12 weeks ago by 53k • written 12 weeks ago by ▴ 60
60
votes
28
replies
7.8k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 8 months ago by 41k • written 9.2 years ago by 99k
59
votes
43
replies
20k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 8 months ago by 41k • written 6.2 years ago by ★ 1.4k
59
votes
25
replies
4.2k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size statistical-power RNA-Seq
updated 5 months ago by 41k • written 3.3 years ago by ▴ 220
59
votes
31
replies
4.4k
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 months ago by 41k • written 6.9 years ago by 10k
58
votes
25
replies
39k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 8 months ago by 41k • written 7.3 years ago by ★ 9.3k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 15 days ago by 41k • written 13.6 years ago by 18k
57
votes
15
replies
4.5k
views
9 follow
Forum: Entice Biologists To Learn R
r
updated 9 months ago by 41k • written 12.2 years ago by 5.3k
57
votes
22
replies
24k
views
7 follow
Batch correction in DESeq2
DESeq2 Batch Effect Combat
updated 8 months ago by 86k • written 4.1 years ago by ▴ 510
57
votes
9
replies
5.5k
views
14 follow
Forum: Handbooks for Bioinformatics Ninjas
gallery
updated 7 months ago by 41k • written 7.5 years ago by ★ 9.3k
57
votes
19
replies
27k
views
6 follow
Forum: Attention: Bowtie2 And Multiple Hits
next-gen bowtie mapping
updated 9 months ago by 41k • written 11.1 years ago by 10k
57
votes
43
replies
15k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
NGS alignment genome RNA-Seq sequence
updated 8 months ago by 41k • written 4.8 years ago by 10k
57
votes
15
replies
5.8k
views
9 follow
Forum: Good practices while dealing with very large datasets
Big-Data Programming
updated 6 months ago by 41k • written 6.6 years ago by ★ 1.1k
1,000 results • Page 4 of 20
Recent Votes
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
Extract UMIs using UMI-tools
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Popular Question to O.rka ▴ 710
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Recent Replies
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by dsull ★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM? by rpolicastro 12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file by ATpoint 78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by ATpoint 78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods by dsull ★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by RNAseqer ▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by Nitin Narwade ★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file by Enrique • 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file by ATpoint 78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
Answer: Generate Read counts from bam file by Enrique • 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts by Brian Bushnell 19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
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