Files for reference-based analysis of transcriptome data
Outline.txt - an outline of steps and options. Start here.
Downloading_and_obtaining_sequence.txt
Download_from_SRA_array.sh will download a list of files from the SRA.
Download_from_SRA.sh will download a single file / project (projects may include many files)
id_list.txt - sample SRA ID list for download
QC.txt
FastQC_array.sh
Trimming.txt
Trim_Galore_array.sh
Trimmomatic_array.sh
Prepare your resources: find your genome, find your annotation (if using), choose your aligner, update your alignment software, and index your genome (before or after 1)
Downloading_and_obtaining_sequence.txt
Index_genome.txt
STAR_index.sh
Alignment.txt
Star_pass_1_array.sh
Star_pass_2_array.sh