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1,000 results • Page 1 of 20
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1.2k
votes
206
replies
53k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 months ago by ★ 1.2k • written 12.5 years ago by 21k
238
votes
176
replies
88k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 4 months ago by 40k • written 8.2 years ago by ★ 4.7k
762
votes
162
replies
123k
views
105 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 6 weeks ago by 2.0k • written 6.8 years ago by 98k
132
votes
123
replies
33k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 5.0 years ago by 86k
298
votes
122
replies
28k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 26 days ago by ▴ 270 • written 13.2 years ago by 11k
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
62
votes
95
replies
17k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 7 months ago by ▴ 10 • written 5.4 years ago by ▴ 260
327
votes
92
replies
226k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 8 weeks ago by ▴ 180 • written 12.7 years ago by 4.9k
77
votes
86
replies
27k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 3 months ago by 40k • written 6.8 years ago by 18k
128
votes
83
replies
11k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression fastq-compressor
updated 3 months ago by 40k • written 6.5 years ago by ★ 2.7k
360
votes
81
replies
140k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
5 months ago by ole.tange ★ 4.3k
118
votes
74
replies
44k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 11 months ago by 134k • written 12.8 years ago by ★ 3.3k
72
votes
71
replies
27k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 3 months ago by 40k • written 5.1 years ago by 86k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
61
votes
70
replies
12k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 7 months ago by 40k • written 9.5 years ago by 98k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 4 weeks ago by ▴ 260 • written 5.9 years ago by 86k
279
votes
69
replies
19k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 7 months ago by 40k • written 12.2 years ago by ▴ 160
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 77k
134
votes
65
replies
4.7k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 3 months ago by 40k • written 3.8 years ago by ▴ 880
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 11 days ago by ▴ 750 • written 12.5 years ago by 4.1k
38
votes
63
replies
18k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 7 months ago by 40k • written 10.7 years ago by 4.2k
144
votes
62
replies
10k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 7 months ago by 40k • written 12.6 years ago by ★ 2.9k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.1 years ago by 86k
117
votes
59
replies
31k
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 7 months ago by 40k • written 8.4 years ago by ▴ 30
361
votes
58
replies
64k
views
44 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
written 13.6 years ago by 98k
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
145
votes
56
replies
7.9k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 7 months ago by 40k • written 10.5 years ago by 98k
290
votes
55
replies
15k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 7 months ago by 40k • written 10.4 years ago by 10k
121
votes
55
replies
95k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 3 days ago by • 0 • written 9.3 years ago by ▴ 340
113
votes
53
replies
5.9k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 4 months ago by 40k • written 4.5 years ago by ▴ 170
54
votes
52
replies
46k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 3 months ago by 40k • written 9.2 years ago by 7.5k
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 years ago by ★ 3.3k
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 3 months ago by 40k • written 9.4 years ago by ▴ 790
26
votes
50
replies
12k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta illumina
updated 3 months ago by 40k • written 7.3 years ago by ▴ 50
27
votes
50
replies
16k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 7 months ago by 40k • written 8.4 years ago by ▴ 610
93
votes
50
replies
15k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 7 months ago by 40k • written 9.9 years ago by 98k
262
votes
48
replies
21k
views
37 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 7 months ago by ★ 1.0k • written 8.4 years ago by ★ 4.2k
39
votes
48
replies
5.8k
views
CUTADAPT in windows
sequencing
updated 7 months ago by 40k • written 8.4 years ago by ★ 4.2k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 7 months ago by 40k • written 10.6 years ago by 33k
72
votes
48
replies
7.6k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 7 months ago by 40k • written 12.5 years ago by 13k
68
votes
48
replies
7.6k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 4 months ago by 40k • written 6.2 years ago by 98k
84
votes
47
replies
30k
views
28 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 days ago by 40k • written 10.0 years ago by ★ 7.7k
188
votes
47
replies
1.7k
views
16 follow
Job: Bioinformatics freelancers needed
freelancer
updated 5 months ago by 40k • written 7.4 years ago by ▴ 190
125
votes
46
replies
46k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 5 months ago by 40k • written 7.6 years ago by ★ 3.2k
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 7 months ago by 40k • written 10.1 years ago by ★ 1.1k
92
votes
46
replies
11k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 7 months ago by 40k • written 12.2 years ago by 3.2k
4
votes
45
replies
6.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 5 months ago by 40k • written 7.3 years ago by ▴ 110
22
votes
45
replies
11k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq next-gen-sequencing
updated 8 months ago by 40k • written 8.4 years ago by ★ 1.1k
102
votes
44
replies
8.3k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 7 months ago by 40k • written 10.1 years ago by 24k
121
votes
44
replies
20k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 7 months ago by 40k • written 13.3 years ago by 5.3k
1,000 results • Page 1 of 20
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: Getting the overlap between two GTF files by Alex Reynolds 35k
What would that be?
Answer: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
@ialbert ,I am deeply immersed in the fog and request the help ,please
Comment: bedtools intersect by position & stand not working even with common regions by rfran010 ▴ 830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files by rfran010 ▴ 830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly. If it's not done alre…
Answer: vcf.gz to vcf by Mark ★ 1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names? by Jiyao Wang ▴ 340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow? by Mark ★ 1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'. Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
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