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3,160 results • Page 1 of 64
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730
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replies
108k
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100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 12 days ago by 1.6k • written 6.3 years ago by 97k
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 2 days ago by 38k • written 8.6 years ago by 20k
274
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 26 days ago by 38k • written 9.4 years ago by 20k
262
votes
48
replies
20k
views
37 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 27 days ago by ▴ 970 • written 7.9 years ago by ★ 4.2k
251
votes
36
replies
30k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 3 days ago by 38k • written 12.9 years ago by 153k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 13 days ago by 38k • written 5.3 years ago by 84k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 4 days ago by ★ 1.1k • written 4.4 years ago by 84k
126
votes
44
replies
27k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 17 days ago by 38k • written 6.5 years ago by ▴ 970
118
votes
26
replies
32k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 16 days ago by ▴ 30 • written 7.9 years ago by ▴ 610
118
votes
53
replies
88k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 330
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 13 days ago by 38k • written 4.7 years ago by 70k
115
votes
35
replies
36k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow Forum
updated 16 days ago by ▴ 30 • written 5.8 years ago by ▴ 760
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 24 days ago by 38k • written 9.1 years ago by ▴ 580
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 26 days ago by 38k • written 9.6 years ago by ★ 1.1k
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 27 days ago by 38k • written 9.6 years ago by 24k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 12 days ago by 38k • written 4.6 years ago by 16k
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 22 days ago by ▴ 20 • written 10.8 years ago by 12k
100
votes
36
replies
27k
views
33 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 4 days ago by ▴ 20 • written 9.4 years ago by ★ 3.6k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 12 days ago by 38k • written 6.6 years ago by 26k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 13 days ago by 2.6k • written 10.8 years ago by ▴ 820
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 25 days ago by 38k • written 9.3 years ago by 97k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 13 days ago by 38k • written 4.6 years ago by 84k
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 25 days ago by 38k • written 9.4 years ago by 20k
84
votes
22
replies
3.4k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 17 days ago by 38k • written 3.8 years ago by ▴ 180
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 17 days ago by 38k • written 4.8 years ago by ★ 1.3k
82
votes
21
replies
14k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 17 days ago by 38k • written 2.4 years ago by 2.9k
81
votes
8
replies
7.8k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 20 days ago by 38k • written 8.8 years ago by 19k
81
votes
21
replies
4.1k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 9 days ago by 38k • written 6.8 years ago by ★ 3.2k
80
votes
23
replies
4.3k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 17 days ago by 38k • written 8.4 years ago by ★ 3.0k
79
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 27 days ago by 38k • written 9.7 years ago by 11k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 12 days ago by 38k • written 5.1 years ago by 84k
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 3 days ago by 38k • written 9.1 years ago by ★ 1.5k
72
votes
18
replies
6.7k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 27 days ago by 38k • written 9.7 years ago by 7.7k
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 24 days ago by 38k • written 9.1 years ago by 97k
67
votes
21
replies
5.0k
views
8 follow
Forum: Meta: Markdown in Biostars (now enabled)
meta
12 days ago by Ram 38k
66
votes
18
replies
46k
views
16 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq tools
updated 13 days ago by • 0 • written 10.1 years ago by ★ 3.6k
66
votes
21
replies
5.6k
views
18 follow
Forum: Is there anyone who was a pure biologist?
next-gen
updated 20 days ago by 38k • written 8.9 years ago by ▴ 100
65
votes
17
replies
30k
views
12 follow
Transform a GTF file into a data frame in R
R RNA-Seq GTF
updated 26 days ago by 38k • written 5.5 years ago by ▴ 350
65
votes
26
replies
18k
views
13 follow
Forum: Macosx For Bioinformatics?
linux
updated 25 days ago by 38k • written 9.3 years ago by 11k
64
votes
3
replies
268k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 20 days ago by 38k • written 8.8 years ago by ▴ 960
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 12 days ago by 38k • written 5.5 years ago by 84k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 13 days ago by 38k • written 4.1 years ago by 16k
61
votes
11
replies
14k
views
9 follow
Forum: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
programming
updated 27 days ago by 38k • written 9.7 years ago by 19k
61
votes
14
replies
19k
views
13 follow
Why is Hadoop not used a lot in bio-informatics?
hadoop
updated 17 days ago by 38k • written 8.5 years ago by ★ 5.2k
60
votes
6
replies
8.9k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 27 days ago by 38k • written 9.6 years ago by 9.5k
60
votes
28
replies
7.3k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 17 days ago by 38k • written 8.5 years ago by 97k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 12 days ago by 38k • written 6.5 years ago by ★ 3.3k
59
votes
43
replies
18k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 12 days ago by 38k • written 5.5 years ago by ★ 1.4k
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 9 days ago by 38k • written 6.7 years ago by ★ 9.3k
58
votes
23
replies
12k
views
11 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 3 days ago by 38k • written 4.1 years ago by ★ 1.1k
3,160 results • Page 1 of 64
Recent Votes
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Comment: Protein name in GenBank
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Recent Replies
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
RNA pol always transcribes 5' -> 3'. This has nothing to do with +/-. Think of it on the DNA level: If the mRNA made is the same sequenc…
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq? by Ming Tommy Tang ★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
Answer: Variant Calling with Multiple Individuals in Freebayes by Ming Tommy Tang ★ 2.9k
It looks like you can provide multiple bam files and output a gVCF file https://github.com/freebayes/freebayes#usage
Answer: Log2 FC Threshold by Ming Tommy Tang ★ 2.9k
This is hard to say. Some genes could play a very different role, even with little change. You want to focus on the large FC genes initiall…
Answer: Log2 FC Threshold by Mensur Dlakic ★ 23k
There is no prescribed logFC that everyone follows. The point is to convince yourself and others - those reviewing your papers and grants -…
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