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353 results • Page 1 of 8
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276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 4 days ago by 38k • written 8.6 years ago by 20k
275
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 28 days ago by 38k • written 9.4 years ago by 20k
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.7 years ago by ★ 4.6k
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 weeks ago by 38k • written 10.5 years ago by 20k
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 4 months ago by 38k • written 9.4 years ago by ★ 1.2k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 14 days ago by 38k • written 2.7 years ago by ▴ 690
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 19 days ago by 38k • written 2.0 years ago by ★ 1.3k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 1.6k
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 29 days ago by 38k • written 9.8 years ago by 11k
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 4 weeks ago by 38k • written 10.0 years ago by 5.9k
0
votes
3
replies
47k
views
Tutorial: Installation VMD on LINUX_64
VMD VMD installation gromacs Tutorial
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 10
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 weeks ago by 38k • written 9.8 years ago by ★ 3.0k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 15 days ago by 38k • written 5.3 years ago by 84k
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 5 weeks ago by 38k • written 11.0 years ago by 11k
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 15 days ago by 38k • written 4.7 years ago by 70k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 14 days ago by 38k • written 6.5 years ago by ★ 3.3k
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 11 days ago by 38k • written 6.7 years ago by ★ 9.3k
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
70
votes
3
replies
34k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 16 months ago by 38k • written 8.7 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 15 days ago by 38k • written 4.6 years ago by 84k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 4 weeks ago by 38k • written 10.5 years ago by 97k
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 27 days ago by 38k • written 9.4 years ago by 20k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 14 days ago by 38k • written 6.6 years ago by 26k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 7 days ago by ★ 1.1k • written 4.4 years ago by 84k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 10 months ago by 38k • written 8.3 years ago by ★ 1.6k
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 months ago by • 0 • written 9.4 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 6 weeks ago by 38k • written 7.1 years ago by 20k
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 6.3 years ago by ▴ 250 • written 7.1 years ago by ★ 1.1k
31
votes
12
replies
26k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 28 days ago by 38k • written 9.4 years ago by 97k
67
votes
6
replies
24k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 26 days ago by 38k • written 9.1 years ago by 97k
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 14 days ago by 38k • written 2.6 years ago by ▴ 140
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 6 weeks ago by 38k • written 5.6 years ago by 84k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 14 days ago by 38k • written 4.6 years ago by 16k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 4 weeks ago by 38k • written 10.2 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 7 months ago by 38k • written 7.5 years ago by ★ 2.3k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 6 months ago by 38k • written 10.9 years ago by 97k
1
vote
1
reply
19k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 8 months ago by ★ 2.5k • written 8 months ago by ▴ 10
10
votes
5
replies
18k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 14 days ago by 38k • written 4.7 years ago by ★ 9.3k
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 14 days ago by 38k • written 5.5 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 13 days ago by 38k • written 6.5 years ago by ▴ 310
41
votes
6
replies
18k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 14 months ago by ▴ 40 • written 2.0 years ago by 11k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
chromosome karyotype R ggplot2 Tutorial
updated 5.3 years ago by ★ 3.4k • written 5.6 years ago by ★ 3.3k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 14 days ago by 38k • written 5.1 years ago by 84k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 14 days ago by 38k • written 6.8 years ago by ▴ 160
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 4 weeks ago by 38k • written 10.1 years ago by 33k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 19 days ago by 38k • written 4.8 years ago by ★ 1.3k
353 results • Page 1 of 8
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Answer: Snakemake vs Nextflow Upcoming bioinformatics Project
Answer: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
Answer: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
Answer: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
Answer: What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
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Answer: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran by Yuri • 0
Hi @and did you ever figure out why guppy was resulting in 90% of reads in unclassified folder? I am running into the same issue, and am…
Comment: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt by ladina.hoesli • 0
Thank you very much, this helps a lot!
Answer: Snakemake vs Nextflow Upcoming bioinformatics Project by cfos4698 ▴ 720
There are a lot of votes for Nextflow here, and it's generally pretty popular (and increasing in popularity). As a 'dissenting' voice, I'll…
Answer: Is it possible to use pseudoalignments.bam to run rMATs? by dsull ★ 4.0k
No, you can't do that with kallisto's bam files. For one, kallisto (by default) doesn't map to introns which is required by rMATs. You c…
Answer: genome annotation [sstart] [send] - how to get protein sequence from gene by shenwei356 8.0k
It means that the gene is on the negative/minus strand. So you need to compute the reverse complementary sequence before translating it to …
Answer: When to merge multiple fastq files into one for RNAseq analysis? by GenoMax 127k
As long as the sample name matches across the lanes they are pieces of the same sample. > I was thinking of combining the two fastq files…
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
Yes, just put that fastq file (it'll be the same as any other kallisto bustools run, except you have just one fastq file and you have that …
Comment: Error building snpEff database "Transcript 'hypothetical_protein' already exist by Jane • 0
Hi, I have the same issue. After running the command, I run the "sh scripts/buildDbNcbi.sh U00096.2" to download again. Then the same issu…
Comment: bash command to process a line by saadleeshehreen ▴ 110
Thanks a lot. It worked
Answer: bash command to process a line by GenoMax 127k
With just one line example not sure if this will work awk -F '[|_]' '{print $2,$4}' your_file CU459141.1 CAM87240.1
Comment: RNA Sequencing and Vg pan -transcriptome build by kcarery • 0
Thank you! I found this as well and trying to understand it now.
Comment: RNA Sequencing and Vg pan -transcriptome build by kcarery • 0
Thank you so much! This is where I am leading back to as well! I don't have much insights into Hisat2. I am going to give it a go this week…
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript by Juke34 7.8k
Interesting, why would you merge genes that are on different strands? They should be different genes. It cannot be done without modifying t…
Comment: featureCounts problem in reading Gff by Beatrice • 0
That's the output, so apparently I have the exon. Anyway, after running grep command the featureCounts worked, even though I didn't change …
Comment: bash command to process a line by saadleeshehreen ▴ 110
Yes the word start with lcl| and always sperated by _prot_. I am very naive pattern matching and extraction. I was trying to cut the field …
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