reference-keys.txt

introduction
contents
data
sequence-reads-to-snp-level-parent-specific-read-counts-1
overview
setup
command-line-tools
amel_hav3.1-reference-genome-assembly-and-annotation-files
a-note-on-parallel-processing-in-high-performance-computing-clusters
generation-of-f1-genomes-and-transcriptomes
wgs-read-pre-processing
retrieve-wgs-reads-from-sra
assess-raw-quality-control-metrics
trim-and-filter-reads
aggregate-qc-reports-with-multiqc
wgs-read-alignment-and-post-processing
generate-bwa-alignment-index-for-the-amel_hav3.1-reference-genome-assembly
align-reads-to-the-amel_hav3.1-reference-genome-assembly-with-bwa-mem
sort-and-filter-alignments-with-samtools-and-filter-duplicates-with-gatk
variant-discovery-and-filtration
genome-and-transcriptome-construction
construct-f1-genomes-with-gatk-fastaalternatereferencemaker
construct-f1-transcriptomes-for-star
annotate-f1-snps-within-genes
quantification-of-f2-allele-specific-transcription
mrna-seq-read-pre-processing
retrieve-mrna-seq-reads-from-sra
assess-raw-quality-control-metrics-1
trim-and-filter-reads-1
aggregate-qc-reports-with-multiqc-1
mrna-seq-read-alignment-to-f1-transcriptomes
mrna-seq-alignment-post-processing-and-allele-specific-read-counting
snp-level-parent-specific-read-counts-to-allele-specific-transcription-1
overview-1
setup-1
tutorial-files
packages
custom-functions
sample-metadata
generate-sample-x-snpgene-count-matrix
filter-snps-by-transcript
merge-count-files-to-matrix
prepare-sample-x-snpgene-counts-for-analysis
normalize-by-library-size
split-by-phenotype-and-filter-low-count-snps
conduct-statistical-tests
snp-level-storer-kim-sk-binomial-exact-tests
gene-level-general-linear-mixed-models-glimmix
allele-specific-transcription-analysis
fdr-correction-and-threshold-tests
chi-squared-tests
data-visualization
session-info