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277
votes
39
replies
168k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 10 weeks ago by 39k • written 8.8 years ago by 20k
277
votes
33
replies
94k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by 39k • written 9.6 years ago by 20k
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 days ago by 39k • written 7.8 years ago by ★ 4.6k
136
votes
25
replies
77k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 14 months ago by 39k • written 11.1 years ago by ★ 4.2k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
74
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 7 months ago by 39k • written 9.5 years ago by ★ 1.2k
45
votes
14
replies
65k
views
10 follow
Tutorial: Using R in Conda
R
updated 11 weeks ago by 39k • written 2.9 years ago by ▴ 690
26
votes
10
replies
63k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 12 weeks ago by 39k • written 2.2 years ago by ★ 1.3k
148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
80
votes
2
replies
54k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by 39k • written 9.9 years ago by 11k
145
votes
34
replies
52k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 3 months ago by 39k • written 10.1 years ago by 5.9k
0
votes
3
replies
48k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 8 weeks ago by 39k • written 7.0 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 3 months ago by 39k • written 9.9 years ago by ★ 3.0k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
51
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 3 months ago by 39k • written 11.1 years ago by 11k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 11 weeks ago by 39k • written 4.9 years ago by 72k
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 3.3k
58
votes
25
replies
37k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 11 weeks ago by 39k • written 6.9 years ago by ★ 9.3k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 weeks ago by 39k • written 4.8 years ago by 85k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 3 months ago by 39k • written 11.2 years ago by ▴ 540
71
votes
3
replies
35k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 18 months ago by 39k • written 8.9 years ago by 98k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 3 months ago by 39k • written 10.7 years ago by 98k
89
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 3 months ago by 39k • written 9.6 years ago by 20k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 11 weeks ago by 39k • written 6.8 years ago by 26k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 13 months ago by 39k • written 8.5 years ago by ★ 1.6k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 27 days ago by 39k • written 9.6 years ago by ★ 7.7k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
1
vote
1
reply
27k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 10 months ago by ★ 2.9k • written 10 months ago by ▴ 10
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 weeks ago by 39k • written 7.3 years ago by ★ 1.1k
31
votes
12
replies
27k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 3 months ago by 39k • written 9.6 years ago by 98k
31
votes
9
replies
26k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 140
70
votes
26
replies
25k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by 39k • written 9.3 years ago by 98k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 11 weeks ago by 39k • written 4.8 years ago by 16k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 3 months ago by 39k • written 10.4 years ago by ▴ 300
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 10 months ago by 39k • written 7.7 years ago by ★ 2.3k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 8 months ago by 39k • written 11.1 years ago by 98k
10
votes
5
replies
19k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 11 weeks ago by 39k • written 4.9 years ago by ★ 9.3k
42
votes
6
replies
19k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 16 months ago by ▴ 40 • written 2.2 years ago by 12k
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 11 weeks ago by 39k • written 5.7 years ago by ★ 1.4k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 11 weeks ago by 39k • written 6.7 years ago by ▴ 310
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 19 days ago by 39k • written 5.8 years ago by ★ 3.3k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 11 weeks ago by 39k • written 5.3 years ago by 85k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 weeks ago by 39k • written 2.6 years ago by 2.9k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 11 weeks ago by 39k • written 6.9 years ago by ▴ 170
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 9 days ago by • 0 • written 5.0 years ago by ★ 1.3k
357 results • Page 1 of 8
Recent Votes
Comment: Is RNA-Seq well suited for studying pseudogenes and lncRNA?
Comment: Is RNA-Seq well suited for studying pseudogenes and lncRNA?
Answer: calculate p value and associated z score for snp-gene pair
Answer: calculate p value and associated z score for snp-gene pair
Answer: I need help with a blast command, please help
Answer: I need help with a blast command, please help
Answer: NCBI API, Perl
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Recent Replies
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
Yes, BED file, so this is zero-based and on Ensembl Viewer it is 1-based. So that is the reason.
Comment: Obtain a --gene-trans-map file after rnaSPAdes by andres.firrincieli 3.3k
Following GenoMax comment This is what you have NODE_217_length_5488_cov_28.472321_g133_i0 # typical rnaSPAdes transcript header Thi…
Comment: calculate p value and associated z score for snp-gene pair by rheab1230 ▴ 140
Thank you so much for this. Yes, in this case I get all the SNPs. I also have one more question: SNP gene beta t-stat p-value FDR …
Comment: Is RNA-Seq well suited for studying pseudogenes and lncRNA? by rpolicastro 12k
lncRNAs are usually fine to include in downstream analysis since they are generally not selected against in most RNA-seq library prep proto…
Comment: I need help with a blast command, please help by neto.pvp • 0
Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!
Answer: NCBI API, Perl by GenoMax 129k
You are likely best served by using `NCBI datasets` ([**LINK**][1]) or `EntrezDirect` ([**LINK**][2]) command line tools. If you want to …
Comment: Obtain a --gene-trans-map file after rnaSPAdes by GenoMax 129k
You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0 While this is from an unrelated software the so…
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
that is another question
Comment: Difference between USCS exon coordinates and ensembl by amy__ ▴ 50
Hi @atpoint, I went to http://genome.ucsc.edu/cgi-bin/hgTables and did: 1. ![enter image description here][1] then: 2. ![enter image…
Comment: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex by Kermit ▴ 80
See also: https://www.biostars.org/p/9535550/#9536086
Answer: Getting species names and taxa id from assembly accession number by MirianT_NCBI ▴ 590
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder by GenoMax 129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output by rpolicastro 12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
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