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383 results • Page
2 of 8
Sort: Views
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Views
Votes
Replies
72
votes
48
replies
17k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 9 months ago by
Ram
41k • written 10.8 years ago by
lh3
33k
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 6 months ago by
GenoMax
136k • written 10.0 years ago by
Obi Griffith
20k
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 9 months ago by
Ram
41k • written 10.8 years ago by
Cyriac Kandoth
6.0k
75
votes
14
replies
15k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 9 months ago by
Ram
41k • written 10.5 years ago by
Medhat
9.7k
16
votes
7
replies
15k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 8 months ago by
Ram
41k • written 4.5 years ago by
atakanekiz
▴ 310
15
votes
5
replies
15k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 7 months ago by
Ram
41k • written 7.5 years ago by
Obi Griffith
20k
76
votes
13
replies
15k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 2.1 years ago by
Ram
41k • written 9.5 years ago by
Malachi Griffith
19k
54
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 14 months ago by
Ram
41k • written 10.0 years ago by
Nicholas Spies
★ 1.2k
16
votes
11
replies
14k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 8 months ago by
Ram
41k • written 7.1 years ago by
TriS
★ 4.7k
11
votes
7
replies
14k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 6 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
86k
13
votes
3
replies
14k
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 3 months ago by
William
▴ 20 • written 6.7 years ago by
kirannbishwa01
★ 1.6k
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 9 months ago by
Ram
41k • written 10.7 years ago by
Obi Griffith
20k
12
votes
20
replies
13k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 8 months ago by
Ram
41k • written 4.5 years ago by
jared.andrews07
★ 16k
63
votes
15
replies
13k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 6 months ago by
Ram
41k • written 5.1 years ago by
finswimmer
16k
65
votes
26
replies
13k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 8 months ago by
Ram
41k • written 4.7 years ago by
finswimmer
16k
19
votes
3
replies
13k
views
Tutorial:
bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 16 months ago by
Ram
41k • written 7.8 years ago by
Shicheng Guo
★ 9.3k
47
votes
19
replies
13k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 10 months ago by
Ram
41k • written 10.8 years ago by
Istvan Albert
99k
64
votes
13
replies
13k
views
11 follow
Tutorial:
Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect
GATK
Picard
Exome
updated 21 months ago by
Ram
41k • written 9.1 years ago by
Chirag Nepal
★ 2.4k
64
votes
26
replies
13k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 8 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
86k
8
votes
19
replies
13k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 8 months ago by
Ram
41k • written 9.0 years ago by
Lesley Sitter
▴ 600
16
votes
0
replies
13k
views
Tutorial:
Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 9 months ago by
Ram
41k • written 11.6 years ago by
David Langenberger
10k
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 7 months ago by
Ram
41k • written 7.7 years ago by
Sinji
★ 3.2k
39
votes
8
replies
12k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
R
methylation
updated 8 months ago by
Ram
41k • written 3.2 years ago by
Hamid Ghaedi
3.1k
15
votes
5
replies
12k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 8 months ago by
Ram
41k • written 6.0 years ago by
ahmad mousavi
▴ 760
43
votes
6
replies
12k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 9 months ago by
Ram
41k • written 9.8 years ago by
Cyriac Kandoth
6.0k
4
votes
13
replies
12k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 5 months ago by
Ram
41k • written 4.8 years ago by
jaybee
▴ 140
28
votes
13
replies
12k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 22 months ago by
liorglic
★ 1.3k • written 2.1 years ago by
Istvan Albert
99k
7
votes
2
replies
11k
views
Tutorial:
Howto use NCBI programs behind a HTTP proxy
blast-plus
HTTP-proxy
SRA-toolkit
updated 16 months ago by
Ram
41k • written 7.8 years ago by
piet
★ 1.8k
40
votes
9
replies
11k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 8 months ago by
Ram
41k • written 9.6 years ago by
Ahill
★ 1.9k
31
votes
6
replies
11k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 8 months ago by
Ram
41k • written 3.5 years ago by
Kevin Blighe
86k
49
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
0
votes
0
replies
11k
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
22 months ago by
Wayne
★ 1.8k
70
votes
5
replies
11k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 20 months ago by
Ram
41k • written 9.6 years ago by
umer.zeeshan.ijaz
★ 1.8k
31
votes
8
replies
11k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 8 months ago by
Ram
41k • written 9.6 years ago by
Rad
▴ 810
8
votes
9
replies
11k
views
Tutorial:
Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq
fasta
updated 8 months ago by
Ram
41k • written 9.6 years ago by
umer.zeeshan.ijaz
★ 1.8k
10
votes
4
replies
10k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 8 months ago by
Ram
41k • written 4.4 years ago by
colindaven
5.7k
10
votes
31
replies
9.9k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 5 weeks ago by
ha2606
• 0 • written 5.9 years ago by
vimalkvn
▴ 320
11
votes
7
replies
9.8k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 6 months ago by
Ram
41k • written 2.7 years ago by
Novogene
▴ 360
18
votes
2
replies
9.8k
views
Tutorial:
Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq
Galaxy
IGB
updated 20 months ago by
Ram
41k • written 9.1 years ago by
Nowlan Freese
▴ 860
14
votes
0
replies
9.3k
views
Tutorial:
How to generate PCA plot and heatmaps in R
heatmap
PCA
RNA-Seq
R
updated 7 months ago by
Ram
41k • written 7.2 years ago by
Ming Tommy Tang
★ 3.6k
48
votes
30
replies
9.3k
views
11 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 28 days ago by
ATpoint
78k • written 7.7 years ago by
Ram
41k
61
votes
6
replies
9.3k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by
Ram
41k • written 10.3 years ago by
Medhat
9.7k
16
votes
5
replies
8.8k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Obi Griffith
20k
19
votes
4
replies
8.7k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 9 months ago by
Ram
41k • written 10.7 years ago by
Istvan Albert
99k
20
votes
0
replies
8.6k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 9 months ago by
Ram
41k • written 11.2 years ago by
Istvan Albert
99k
10
votes
1
reply
8.6k
views
Tutorial:
How to select reads with specific flag using samtools
next-gen-sequencing
updated 6 months ago by
Ram
41k • written 6.2 years ago by
imlituan
▴ 110
25
votes
15
replies
8.6k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 9 months ago by
Ram
41k • written 10.9 years ago by
Medhat
9.7k
9
votes
0
replies
8.5k
views
Tutorial:
Installing And Running Ncbi Blast
blast
updated 9 months ago by
Ram
41k • written 11.6 years ago by
MSU course 2011
▴ 540
3
votes
2
replies
8.4k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 6 months ago by
Ram
41k • written 6.0 years ago by
chen
★ 2.5k
20
votes
4
replies
8.4k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 7 months ago by
Ram
41k • written 7.2 years ago by
fi1d18
★ 4.2k
383 results • Page
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Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
Extract UMIs using UMI-tools
Answer: Good alignment rate for DNA-seq data
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Comment: frequency plot for peaks
by
Ankit
▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
cmdcolin
★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
rpolicastro
12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file
by
ATpoint
78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
ATpoint
78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods
by
dsull
★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
RNAseqer
▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
Nitin Narwade
★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file
by
Enrique
• 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file
by
ATpoint
78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
Answer: Generate Read counts from bam file
by
Enrique
• 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts
by
Brian Bushnell
19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
Answer: bam or VCF files from GSE75010
by
ATpoint
78k
It's a gene expression **array**, not RNA-seq. Arrays do not allow variant calling as there is no digital sequencing data created.
Answer: Generate Read counts from bam file
by
ATpoint
78k
I don't follow. You always align to the full genome (which includes the mt genome in case of human reference genomes). Anyway, if you g…
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