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1,000 results • Page 1 of 20
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1.2k
votes
206
replies
54k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 6 months ago by ★ 1.3k • written 12.7 years ago by 22k
238
votes
176
replies
90k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 months ago by 41k • written 8.3 years ago by ★ 4.7k
772
votes
164
replies
128k
views
107 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 8 weeks ago by 2.3k • written 7.0 years ago by 99k
132
votes
123
replies
34k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
298
votes
122
replies
29k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 12 weeks ago by ▴ 270 • written 13.4 years ago by 11k
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.2 years ago by 86k
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
328
votes
92
replies
230k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 3 months ago by ▴ 190 • written 12.8 years ago by 4.9k
77
votes
86
replies
28k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 5 months ago by 41k • written 7.0 years ago by 19k
128
votes
83
replies
12k
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 5 months ago by 41k • written 6.7 years ago by ★ 2.7k
361
votes
81
replies
141k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
7 months ago by ole.tange ★ 4.4k
72
votes
71
replies
28k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 5 months ago by 41k • written 5.2 years ago by 86k
76
votes
70
replies
18k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 8 months ago by 41k • written 5.8 years ago by 86k
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
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
279
votes
69
replies
19k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 9 months ago by 41k • written 12.3 years ago by ▴ 160
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 months ago by 41k • written 5.4 years ago by 78k
134
votes
65
replies
5.1k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 5 months ago by 41k • written 4.0 years ago by ▴ 880
162
votes
64
replies
82k
views
39 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 10 weeks ago by ▴ 780 • written 12.7 years ago by 4.1k
38
votes
63
replies
19k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 9 months ago by 41k • written 10.8 years ago by 4.2k
144
votes
62
replies
11k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 9 months ago by 41k • written 12.7 years ago by ★ 2.9k
73
votes
60
replies
26k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 9 months ago by 41k • written 6.2 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 9 months ago by 41k • written 8.6 years ago by ▴ 30
361
votes
58
replies
66k
views
44 follow
Forum: Recommend Your Favorite Bioinformatics Books
education books
updated 5 weeks ago by 41k • written 13.7 years ago by 99k
206
votes
58
replies
40k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
121
votes
56
replies
97k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 8 weeks ago by ▴ 20 • written 9.5 years ago by ▴ 340
145
votes
56
replies
8.3k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 9 months ago by 41k • written 10.7 years ago by 99k
290
votes
55
replies
15k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 9 months ago by 41k • written 10.6 years ago by 10k
328
votes
54
replies
61k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 21 days ago by 41k • written 13.7 years ago by 24k
113
votes
53
replies
6.3k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 6 months ago by 41k • written 4.6 years ago by ▴ 170
54
votes
52
replies
47k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 5 months ago by 41k • written 9.3 years ago by 7.5k
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
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
27
votes
50
replies
17k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 9 months ago by 41k • written 8.6 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 9 months ago by 41k • written 10.0 years ago by 99k
26
votes
50
replies
13k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta illumina
updated 5 months ago by 41k • written 7.5 years ago by ▴ 50
85
votes
49
replies
9.4k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 21 days ago by 41k • written 13.7 years ago by 3.4k
262
votes
48
replies
22k
views
37 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 9 months ago by ★ 1.0k • written 8.5 years ago by ★ 4.2k
72
votes
48
replies
17k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 9 months ago by 41k • written 10.8 years ago by 33k
72
votes
48
replies
7.9k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 9 months ago by 41k • written 12.6 years ago by 13k
68
votes
48
replies
8.0k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 6 months ago by 41k • written 6.4 years ago by 99k
39
votes
48
replies
6.1k
views
CUTADAPT in windows
sequencing
updated 9 months ago by 41k • written 8.6 years ago by ★ 4.2k
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 26 days ago by 41k • written 10.1 years ago by ★ 7.8k
188
votes
47
replies
2.1k
views
16 follow
Job: Bioinformatics freelancers needed
freelancer
updated 7 months ago by 41k • written 7.6 years ago by ▴ 190
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 9 months ago by 41k • written 10.3 years ago by ★ 1.1k
125
votes
46
replies
47k
views
21 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 7 months ago by 41k • written 7.7 years ago by ★ 3.2k
92
votes
46
replies
11k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 9 months ago by 41k • written 12.4 years ago by 3.2k
175
votes
46
replies
18k
views
26 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
9 days ago by Istvan Albert 99k
22
votes
45
replies
12k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq next-gen-sequencing
updated 10 months ago by 41k • written 8.5 years ago by ★ 1.2k
185
votes
45
replies
31k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline general
updated 6 weeks ago by 41k • written 13.8 years ago by 28k
1,000 results • Page 1 of 20
Recent Votes
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
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:
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Recent Awards • All
Popular Question to applepie • 0
Popular Question to saipra003 ▴ 10
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Recent Replies
Comment: AttributeError: module 'collections' has no attribute 'Hashable' by jiyoung ▴ 20
Currently I am experiencing the same problem. Have you solved this?
Comment: Help doing differential expression analysis -experimental design and gProfiler T by rajabolacuan • 0
Good Information Sir
Answer: Viral genes not showing up in combined mouse+virus alignment by cook.675 ▴ 200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads by cee28 • 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by GenoMax 136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads by GenoMax 136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu by CTLong ▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
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?
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