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358 results • Page
2 of 8
Sort: Views
Rank
Views
Votes
Replies
72
votes
48
replies
16k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 3 months ago by
Ram
39k • written 10.3 years ago by
lh3
33k
34
votes
17
replies
15k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 5 weeks ago by
GenoMax
130k • written 9.6 years ago by
Obi Griffith
20k
30
votes
14
replies
15k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 3 months ago by
Ram
39k • written 10.3 years ago by
Cyriac Kandoth
5.9k
76
votes
13
replies
14k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 20 months ago by
Ram
39k • written 9.0 years ago by
Malachi Griffith
19k
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 4 months ago by
Ram
39k • written 10.1 years ago by
Medhat
9.6k
53
votes
5
replies
14k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 8 months ago by
Ram
39k • written 9.5 years ago by
Nicholas Spies
★ 1.2k
15
votes
5
replies
14k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 9 weeks ago by
Ram
39k • written 7.0 years ago by
Obi Griffith
20k
16
votes
11
replies
13k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 12 weeks ago by
Ram
39k • written 6.6 years ago by
TriS
★ 4.6k
11
votes
7
replies
13k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 23 days ago by
Ram
39k • written 5.7 years ago by
Kevin Blighe
85k
20
votes
4
replies
13k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 3 months ago by
Ram
39k • written 10.2 years ago by
Obi Griffith
20k
16
votes
7
replies
13k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 12 weeks ago by
Ram
39k • written 4.0 years ago by
atakanekiz
▴ 310
63
votes
13
replies
12k
views
11 follow
Tutorial:
Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect
GATK
Picard
Exome
updated 16 months ago by
Ram
39k • written 8.6 years ago by
Chirag Nepal
★ 2.3k
47
votes
19
replies
12k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 4 months ago by
Ram
39k • written 10.3 years ago by
Istvan Albert
98k
8
votes
19
replies
12k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 3 months ago by
Ram
39k • written 8.6 years ago by
Lesley Sitter
▴ 580
16
votes
0
replies
12k
views
Tutorial:
Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 3 months ago by
Ram
39k • written 11.2 years ago by
David Langenberger
9.9k
44
votes
3
replies
12k
views
Tutorial:
A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics
computational-biology
updated 9 weeks ago by
Ram
39k • written 7.2 years ago by
Sinji
★ 3.2k
59
votes
15
replies
12k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 14 days ago by
Ram
39k • written 4.7 years ago by
finswimmer
16k
12
votes
20
replies
12k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 12 weeks ago by
Ram
39k • written 4.0 years ago by
jared.andrews07
★ 14k
18
votes
3
replies
12k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 10 months ago by
Ram
39k • written 7.3 years ago by
Shicheng Guo
★ 9.3k
64
votes
26
replies
12k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 12 weeks ago by
Ram
39k • written 5.7 years ago by
Kevin Blighe
85k
65
votes
26
replies
12k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 12 weeks ago by
Ram
39k • written 4.3 years ago by
finswimmer
16k
43
votes
6
replies
11k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 3 months ago by
Ram
39k • written 9.4 years ago by
Cyriac Kandoth
5.9k
15
votes
5
replies
11k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 3 months ago by
Ram
39k • written 5.5 years ago by
ahmad mousavi
▴ 750
7
votes
2
replies
11k
views
Tutorial:
Howto use NCBI programs behind a HTTP proxy
blast-plus
HTTP-proxy
SRA-toolkit
updated 10 months ago by
Ram
39k • written 7.3 years ago by
piet
★ 1.8k
48
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 3 months ago by
Ram
39k • written 10.8 years ago by
Istvan Albert
98k
40
votes
9
replies
11k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 3 months ago by
Ram
39k • written 9.2 years ago by
Ahill
★ 1.9k
70
votes
5
replies
10k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 14 months ago by
Ram
39k • written 9.2 years ago by
umer.zeeshan.ijaz
★ 1.8k
30
votes
8
replies
10k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 3 months ago by
Ram
39k • written 9.2 years ago by
Rad
▴ 800
8
votes
9
replies
10k
views
Tutorial:
Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq
fasta
updated 3 months ago by
Ram
39k • written 9.2 years ago by
umer.zeeshan.ijaz
★ 1.8k
38
votes
8
replies
10k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
R
methylation
updated 3 months ago by
Ram
39k • written 2.7 years ago by
Hamid Ghaedi
2.9k
3
votes
13
replies
10k
views
Tutorial:
Merging multiple vcf files into Single vcf file
merge
vcf
bcftools
updated 3 months ago by
Ram
39k • written 4.3 years ago by
jaybee
▴ 140
18
votes
2
replies
9.6k
views
Tutorial:
Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq
Galaxy
IGB
updated 14 months ago by
Ram
39k • written 8.6 years ago by
Nowlan Freese
▴ 860
31
votes
6
replies
9.5k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 12 weeks ago by
Ram
39k • written 3.1 years ago by
Kevin Blighe
85k
0
votes
0
replies
9.5k
views
Tutorial:
Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter
Python
pattern
17 months ago by
Wayne
★ 1.8k
10
votes
4
replies
9.5k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 12 weeks ago by
Ram
39k • written 3.9 years ago by
colindaven
4.9k
60
votes
6
replies
9.0k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 3 months ago by
Ram
39k • written 9.8 years ago by
Medhat
9.6k
14
votes
0
replies
9.0k
views
Tutorial:
How to generate PCA plot and heatmaps in R
heatmap
PCA
RNA-Seq
R
updated 8 weeks ago by
Ram
39k • written 6.7 years ago by
Ming Tommy Tang
★ 2.9k
9
votes
23
replies
8.6k
views
7 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 21 days ago by
Ram
39k • written 5.4 years ago by
vimalkvn
▴ 310
19
votes
4
replies
8.5k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 3 months ago by
Ram
39k • written 10.3 years ago by
Istvan Albert
98k
16
votes
5
replies
8.5k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 3 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
20
votes
0
replies
8.4k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 3 months ago by
Ram
39k • written 10.8 years ago by
Istvan Albert
98k
27
votes
13
replies
8.3k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 16 months ago by
liorglic
★ 1.2k • written 20 months ago by
Istvan Albert
98k
9
votes
0
replies
8.2k
views
Tutorial:
Installing And Running Ncbi Blast
blast
updated 3 months ago by
Ram
39k • written 11.2 years ago by
MSU course 2011
▴ 540
20
votes
4
replies
8.2k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 8 weeks ago by
Ram
39k • written 6.7 years ago by
fi1d18
★ 4.2k
24
votes
15
replies
8.1k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 3 months ago by
Ram
39k • written 10.4 years ago by
Medhat
9.6k
14
votes
0
replies
8.0k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 14 months ago by
Ram
39k • written 8.4 years ago by
Nowlan Freese
▴ 860
81
votes
8
replies
8.0k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 3 months ago by
Ram
39k • written 9.0 years ago by
Malachi Griffith
19k
3
votes
3
replies
8.0k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 21 days ago by
Ram
39k • written 5.5 years ago by
Wenhu_Cao
▴ 100
2
votes
2
replies
7.9k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 22 days ago by
Ram
39k • written 5.5 years ago by
chen
★ 2.4k
8
votes
7
replies
7.8k
views
Tutorial:
Getting Cegma/Genewise To Work On Centos, Rhel
centos
genewise
rhel
cegma
updated 16 months ago by
Ram
39k • written 9.5 years ago by
Adrian Pelin
★ 2.6k
358 results • Page
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Comment: conda: command not found: gatk.
by
bestone
▴ 10
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
155k
> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk.
by
bestone
▴ 10
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
155k
how about all your previous questions ? take a time to validate the good answers (green mark on the left). https://www.biostars.org/p/9565…
Answer: No @hd header returned in sam file when running bwa mem
by
Pierre Lindenbaum
155k
the HD header is not generated by bwa, but you can add it using awk: bwa (...) | awk '(NR==1) {printf("@HD\tVN:1.6\tSO:unknown\n");}{…
Comment: Ensembl vep singularity
by
Kiran
▴ 80
Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?
Answer: No @hd header returned in sam file when running bwa mem
by
GokalpC
▴ 80
Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort. ANGSD…
Comment: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★ 23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome
by
Andy
• 0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★ 23k
If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
Comment: How to get information about promoter from bulk-RNAseq?
by
rfran010
▴ 170
I'll just add what I did with my own dataset of ribo depleted RNA-seq: I took predicted enhancer-promoter interaction datasets from UCSC a…
Answer: How to get information about promoter from bulk-RNAseq?
by
rfran010
▴ 170
What type of RNA-seq data do you have? With polyA, I think it will be hard to incorporate enhancer info without additional datasets. …
Comment: Reorder GO terms using R
by
hellokwmin
• 0
Thank you so much. It worked perfectly.
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Thank you so much, Gordon!
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴ 170
Yes, it is a lot to take in. In your input json, is "atac.fastqs_wt_rep2_R2" valid? This key should match exactly what is given in the exa…
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