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Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

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.github
 
 
.idea
.idea
 
 
_static
_static
 
 
_templates
_templates
 
 
admin
admin
 
 
figures
figures
 
 
files
files
 
 
for-instructors
for-instructors
 
 
jetstream
jetstream
 
 
rob_map
rob_map
 
 
rob_quant
rob_quant
 
 
.DS_Store
.DS_Store
 
 
.ftpconfig
.ftpconfig
 
 
.gitignore
.gitignore
 
 
00_intro_organization.rst
00_intro_organization.rst
 
 
01_Download_and_test.rst
01_Download_and_test.rst
 
 
02_working_with_archives.rst
02_working_with_archives.rst
 
 
03_the_filesystem.rst
03_the_filesystem.rst
 
 
04_DataFilesAndScripts.rst
04_DataFilesAndScripts.rst
 
 
ChandlerDeSeq.rst
ChandlerDeSeq.rst
 
 
DeSeq2_Salmon_Tutorial.md
DeSeq2_Salmon_Tutorial.md
 
 
GATK_pipeline.md
GATK_pipeline.md
 
 
GWAS.md
GWAS.md
 
 
GenomicsShell.rst
GenomicsShell.rst
 
 
IntroductionControlFlowR.md
IntroductionControlFlowR.md
 
 
IntroductionControlFlowR.rst
IntroductionControlFlowR.rst
 
 
LC-github.rst
LC-github.rst
 
 
MacManesTrimming.rst
MacManesTrimming.rst
 
 
MacManes_AssemblyQuest.rst
MacManes_AssemblyQuest.rst
 
 
MacManes_BUSCO.rst
MacManes_BUSCO.rst
 
 
MacManes_MapQuest.rst
MacManes_MapQuest.rst
 
 
MacManes_Trinity.rst
MacManes_Trinity.rst
 
 
MacManes_UNIX.rst
MacManes_UNIX.rst
 
 
MacManes_adventure_week1.rst
MacManes_adventure_week1.rst
 
 
MacManes_adventure_week2.rst
MacManes_adventure_week2.rst
 
 
MacManes_kallisto.rst
MacManes_kallisto.rst
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
R_Introductory_tutorial_2015.md
R_Introductory_tutorial_2015.md
 
 
Read_&_munge_NGS_tutorial.R
Read_&_munge_NGS_tutorial.R
 
 
Read_group_info.md
Read_group_info.md
 
 
Rintro.rst
Rintro.rst
 
 
SOAPdeNovoTrans_count_eXpress.rst
SOAPdeNovoTrans_count_eXpress.rst
 
 
analyzing_drosophila_htseq.rst
analyzing_drosophila_htseq.rst
 
 
analyzing_nanopore_data.rst
analyzing_nanopore_data.rst
 
 
analyzing_nanopore_data_Loman.rst
analyzing_nanopore_data_Loman.rst
 
 
arabidopsis_assembly_challenge.rst
arabidopsis_assembly_challenge.rst
 
 
assembling-ecoli.rst
assembling-ecoli.rst
 
 
automation-2.md
automation-2.md
 
 
bcl2fastq.rst
bcl2fastq.rst
 
 
code-of-conduct.rst
code-of-conduct.rst
 
 
command-line-and-rstudio.md
command-line-and-rstudio.md
 
 
conf.py
conf.py
 
 
counting.md
counting.md
 
 
day1.rst
day1.rst
 
 
day2.rst
day2.rst
 
 
densityCurves.R
densityCurves.R
 
 
drosophila_htseq.R
drosophila_htseq.R
 
 
drosophila_rnaseq1.rst
drosophila_rnaseq1.rst
 
 
drosophila_rnaseq_bwa_htseq.rst
drosophila_rnaseq_bwa_htseq.rst
 
 
drosophila_rnaseq_counting_htseq.rst
drosophila_rnaseq_counting_htseq.rst
 
 
eel-pond.rst
eel-pond.rst
 
 
filezila-file-transfer.md
filezila-file-transfer.md
 
 
functional_annotation.rst
functional_annotation.rst
 
 
functional_annotation_2016.rst
functional_annotation_2016.rst
 
 
genome-assembly.md
genome-assembly.md
 
 
genome-comparison-and-phylogeny.rst
genome-comparison-and-phylogeny.rst
 
 
genome_tophat_htseq_counts.zip
genome_tophat_htseq_counts.zip
 
 
git-koans.rst
git-koans.rst
 
 
howe-mgrast.rst
howe-mgrast.rst
 
 
howe-ncbi.rst
howe-ncbi.rst
 
 
index.md
index.md
 
 
instructors-guide.rst
instructors-guide.rst
 
 
interval-analysis-and-visualization.rst
interval-analysis-and-visualization.rst
 
 
introduction-to-R-and-dataframes.md
introduction-to-R-and-dataframes.md
 
 
introduction-to-automation.md
introduction-to-automation.md
 
 
jupyter_notebook.rst
jupyter_notebook.rst
 
 
kmers-and-sourmash.md
kmers-and-sourmash.md
 
 
kmers-etc.rst
kmers-etc.rst
 
 
kraken_species_identification.rst
kraken_species_identification.rst
 
 
linuxbrew_install.rst
linuxbrew_install.rst
 
 
live-coding-test.txt
live-coding-test.txt
 
 
long-and-short-reads.md
long-and-short-reads.md
 
 
long-read.rst
long-read.rst
 
 
meta_GWAS.md
meta_GWAS.md
 
 
mount_chris_snapshot.rst
mount_chris_snapshot.rst
 
 
pop_gen_tutorial.rst
pop_gen_tutorial.rst
 
 
prokka_genome_annotation.rst
prokka_genome_annotation.rst
 
 
quality-trimming.md
quality-trimming.md
 
 
requirements.txt
requirements.txt
 
 
rnaseq_mapping_to_transcritome_bwa_htseq_counts.tar.gz
rnaseq_mapping_to_transcritome_bwa_htseq_counts.tar.gz
 
 
running-blast-large-scale.md
running-blast-large-scale.md
 
 
running-command-line-blast.md
running-command-line-blast.md
 
 
sam-format-tutorial.rst
sam-format-tutorial.rst
 
 
setup.rst
setup.rst
 
 
short-read-quality-evaluation-ctb.rst
short-read-quality-evaluation-ctb.rst
 
 
short-read-quality-evaluation.rst
short-read-quality-evaluation.rst
 
 
toc.rst
toc.rst
 
 
transrate.rst
transrate.rst
 
 
variant-calling.md
variant-calling.md
 
 

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