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282
votes
39
replies
173k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 6 months ago by 40k • written 9.9 years ago by 20k
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 8.1 years ago by ★ 4.7k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 10 weeks ago by • 0 • written 5.2 years ago by ▴ 580
137
votes
25
replies
79k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 17 months ago by 40k • written 11.4 years ago by ★ 4.2k
50
votes
14
replies
74k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 8 months ago by 40k • written 11.0 years ago by 20k
27
votes
10
replies
69k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 10 months ago by 40k • written 9.8 years ago by ★ 1.2k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 7 months ago by 40k • written 10.8 years ago by ★ 1.6k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 6 months ago by 40k • written 10.2 years ago by 11k
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 6 months ago by 40k • written 10.4 years ago by 6.0k
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 months ago by 40k • written 10.2 years ago by ★ 3.0k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 24 days ago by ▴ 260 • written 5.8 years ago by 86k
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 76k
53
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 7 months ago by 40k • written 11.4 years ago by 11k
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
2
votes
1
reply
40k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 14 months ago by 3.7k • written 14 months ago by ▴ 20
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
58
votes
25
replies
38k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 6 months ago by 40k • written 7.2 years ago by ★ 9.3k
72
votes
3
replies
36k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 22 months ago by 40k • written 9.2 years ago by 98k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 7 months ago by 40k • written 11.5 years ago by ▴ 540
132
votes
123
replies
32k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 4.9 years ago by 86k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 7 months ago by 40k • written 11.0 years ago by 98k
99
votes
16
replies
31k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.1 years ago by 26k
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 6 months ago by 40k • written 9.9 years ago by 20k
82
votes
43
replies
30k
views
26 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 12 weeks ago by ▴ 40 • written 9.9 years ago by ★ 7.7k
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 weeks ago by • 0 • written 7.5 years ago by 20k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 16 months ago by 40k • written 8.8 years ago by ★ 1.6k
31
votes
12
replies
28k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 6 months ago by 40k • written 9.9 years ago by 98k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 5 months ago by 40k • written 7.6 years ago by ★ 1.1k
71
votes
26
replies
26k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 6 months ago by 40k • written 9.6 years ago by 98k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
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 6.0 years ago by 86k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
42
votes
16
replies
22k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 13 months ago by 40k • written 8.0 years ago by ★ 2.4k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 7 months ago by 40k • written 10.7 years ago by ▴ 300
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 12 months ago by 40k • written 11.4 years ago by 98k
43
votes
6
replies
21k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 20 months ago by ▴ 40 • written 2.5 years ago by 12k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 6 months ago by 40k • written 5.2 years ago by ★ 9.3k
59
votes
43
replies
19k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 6 months ago by 40k • written 6.0 years ago by ★ 1.4k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 6 months ago by 40k • written 7.0 years ago by ▴ 310
84
votes
21
replies
18k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 2.9 years ago by 3.0k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 4 months ago by 40k • written 6.1 years ago by ★ 3.3k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
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
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.2 years ago by ▴ 170
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 3 months ago by • 0 • written 5.3 years ago by ★ 1.3k
379 results • Page 1 of 8
Recent Votes
Answer: How to retrieve LoF and missense variants in WES data?
Answer: How to retrieve LoF and missense variants in WES data?
Answer: How to check RNAseq support for annotated genes?
Answer: How to check RNAseq support for annotated genes?
A: Remove cells from Seurat based on a list
Remove cells from Seurat based on a list
Comment: kallisto normalized TPM values without bootstraps
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Recent Awards • All
Scholar to ATpoint 76k
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Recent Replies
Comment: Trimmomatic .jar not included anymore? by Pierre Lindenbaum 157k
please review all your previous questions and validate the correct answers (green tick on the left): https://www.biostars.org/p/9575583 htt…
Answer: Trimmomatic .jar not included anymore? by Pierre Lindenbaum 157k
> The command I used to run trimmomatic is this java -jar /storage/home/sjw6257/tools/Trimmomatic-0.39/ java -jar argument should be a f…
Comment: Trimmomatic .jar not included anymore? by petebio ▴ 80
I am guessing that you actually downloaded the source files and not the compiled binary which is why you are missing the .jar file? If this…
Answer: Highly inflated p-values in GWAS by regenie by SushiRoll ▴ 110
Hi! Just jumping in with a suggestion rather than an answer, could it be that the p-values you're getting are not adjusted for multiple com…
Comment: kallisto normalized TPM values without bootstraps by butterman16 ▴ 10
Thank you! Not really sure why I assumed the values had to come from sleuth, but tximport/DESeq2 worked great!
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
before we dive in too deep let's confirm we are on the same page that gnomad 2.1.1 (in your text) is in hg37. gnomad 3.1.2 (in your screens…
Comment: Finding sequences in unannotated genomes using reference coordinates by Pierre Lindenbaum 157k
related: https://www.biostars.org/p/49627
Comment: Finding sequences in unannotated genomes using reference coordinates by Prangan ▴ 20
All done! Thanks.
Comment: Finding sequences in unannotated genomes using reference coordinates by Pierre Lindenbaum 157k
Please review all your previous questions and comment or validate them (green tick on the left) : https://www.biostars.org/p/9568243 https…
Comment: Dealing with transcriptome sequences that are smaller than their respective gene by langziv ▴ 50
How is it possible to tell in case of a mis assembly?
Comment: Salmon alignment based quantification by Mat ▴ 60
I was able to remove the warnings (which eventually ended up in an error) by creating transcriptome file from the genome and it's annotatio…
Comment: Salmon index not progressing by Michael 53k
Are you a student or employe at a university or research institute? In this case it is worth checking with your IT department if there is a…
Comment: Salmon index not progressing by Michael 53k
I think you should kill one of the processes, possibly the decoy one. Also keep an eye on the CPU temperature and the kernel_task. If CPU u…
Comment: ATAC-seq troubleshoot - Just Noise by ATpoint 76k
We use the OmniATAC protocol, which is an enhanced version. Celltype usually does not matter. Based on many years with this assay I can say…
Comment: ATAC-seq troubleshoot - Just Noise by vk ▴ 40
We used U2OS cells and followed the protocol given [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/).
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