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287
votes
39
replies
183k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 13 months ago by 43k • written 9.6 years ago by 20k
296
votes
33
replies
108k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 13 months ago by 43k • written 10.5 years ago by 20k
239
votes
176
replies
94k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 10 months ago by 43k • written 8.7 years ago by ★ 4.7k
93
votes
23
replies
91k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 12 weeks ago by • 0 • written 5.7 years ago by ▴ 610
54
votes
14
replies
91k
views
10 follow
Tutorial: Using R in Conda
R
updated 13 months ago by 43k • written 3.7 years ago by ▴ 840
139
votes
25
replies
83k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 2.0 years ago by 43k • written 12.0 years ago by ★ 4.2k
30
votes
10
replies
81k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 13 months ago by 43k • written 3.1 years ago by ★ 1.6k
196
votes
44
replies
71k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 15 months ago by 43k • written 11.6 years ago by 20k
75
votes
13
replies
67k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 17 months ago by 43k • written 10.4 years ago by ★ 1.2k
149
votes
35
replies
62k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 13 months ago by 43k • written 11.4 years ago by ★ 1.6k
2
votes
1
reply
59k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 21 months ago by 4.2k • written 21 months ago by ▴ 20
87
votes
2
replies
59k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 13 months ago by 43k • written 10.8 years ago by 11k
147
votes
34
replies
54k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 13 months ago by 43k • written 11.0 years ago by 6.0k
0
votes
3
replies
52k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 12 months ago by 43k • written 7.9 years ago by ▴ 10
149
votes
70
replies
50k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 7 months ago by ▴ 260 • written 6.4 years ago by 87k
66
votes
9
replies
49k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 14 months ago by 43k • written 10.8 years ago by ★ 3.0k
117
votes
66
replies
46k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 13 months ago by 43k • written 5.8 years ago by 81k
98
votes
106
replies
46k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 9 days ago by ▴ 20 • written 5.6 years ago by 87k
53
votes
19
replies
43k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 14 months ago by 43k • written 12.0 years ago by 11k
60
votes
52
replies
43k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 13 months ago by 43k • written 7.6 years ago by ★ 3.5k
58
votes
25
replies
40k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 13 months ago by 43k • written 7.7 years ago by ★ 9.4k
74
votes
3
replies
39k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.4 years ago by 43k • written 9.7 years ago by 100k
133
votes
123
replies
38k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 13 months ago by ★ 1.2k • written 5.5 years ago by 87k
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 14 months ago by 43k • written 12.0 years ago by ▴ 540
39
votes
16
replies
36k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 3 months ago by 141k • written 3.7 years ago by ▴ 160
99
votes
16
replies
33k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 13 months ago by 43k • written 7.7 years ago by 27k
90
votes
48
replies
33k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 5 months ago by 43k • written 10.5 years ago by ★ 7.8k
95
votes
25
replies
33k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 14 months ago by 43k • written 11.6 years ago by 100k
90
votes
19
replies
32k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 13 months ago by 43k • written 10.5 years ago by 20k
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 months ago by • 0 • written 8.1 years ago by 20k
142
votes
21
replies
30k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 23 months ago by 43k • written 9.4 years ago by ★ 1.6k
34
votes
12
replies
30k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 13 months ago by 43k • written 10.5 years ago by 100k
99
votes
8
replies
29k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 12 months ago by 43k • written 8.1 years ago by ★ 1.1k
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by • 0 • written 10.2 years ago by 100k
73
votes
60
replies
27k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 14 months ago by 43k • written 6.6 years ago by 87k
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 13 months ago by 43k • written 5.6 years ago by 16k
44
votes
6
replies
24k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 2.2 years ago by ▴ 40 • written 3.1 years ago by 13k
42
votes
16
replies
23k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 20 months ago by 43k • written 8.6 years ago by ★ 2.4k
10
votes
5
replies
23k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by 43k • written 5.7 years ago by ★ 9.4k
85
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 hours ago by • 0 • written 3.5 years ago by 3.2k
51
votes
3
replies
23k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 13 months ago by 43k • written 11.3 years ago by ▴ 300
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 19 months ago by 43k • written 12.0 years ago by 100k
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 13 months ago by 43k • written 6.6 years ago by ★ 1.4k
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 29 days ago by ▴ 30 • written 7.5 years ago by ▴ 310
14
votes
3
replies
20k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 8 months ago by ▴ 30 • written 7.0 years ago by ★ 1.6k
39
votes
6
replies
19k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 11 months ago by 43k • written 6.6 years ago by ★ 3.5k
76
votes
70
replies
19k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 13 months ago by 43k • written 6.2 years ago by 87k
83
votes
34
replies
18k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 10 months ago by • 0 • written 5.8 years ago by ★ 1.3k
18
votes
40
replies
18k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.8 years ago by • 0 • written 7.8 years ago by ▴ 170
408 results • Page 1 of 9
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Can I liftover hs37d5 to hg38 using hg19ToHg38 chain file?
Comment: Removing duplicates
Comment: Removing duplicates
High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
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Recent Replies
Comment: Removing duplicates by quentinperriere • 0
thank you for responding. I was looking for suitable variant calling tool. I'm working on fungus and I don't have fast5 files. Could you re…
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results? by LChart 3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error? by 22211020193 • 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates by joe ▴ 500
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates by samuel.a.odonnell ▴ 520
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis by geneontologyhelp ▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data? by etiennedanis ▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates by joe ▴ 500
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together? by GenoMax 141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions by swbarnes2 14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates by quentinperriere • 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
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