TESecondaryStructure

Scripts for determining secondary structure among feature types

Secondary Structure Analysis and MFE Statistics

1. Seperate annotation by featuretypes, and generate unique feature id's, and generate bed files.

siRNA Mappings

1. Download siRNA libraries
2. Trim using sbatch_trimmomatic.sh
3. Extract 21, 22, 24 length reads sbatch_extract_readsonlen.sh
4. Convert 21, 22, 24 fasta's to unique fasta files with counts added to header. sbatch_generate_ucountsfasta
5. Build reference fasta file index. sbatch_bowtiebuild.sh
6. Align exact matches to reference fasta file. sbatch_bowtie2.sh
7. Convert sam to bam files. sbatch_samtools.sh
8. Filter out mapped and unmapped alignments. sbatch_samtools_filter.sh
9. Sort and index mapped files. sbatch_samtools_sort.sh
10. Convert bam file to bed file and compress. sbatch_bam2bed.sh
11. Sort bed files. sbatch_sortbed.sh
12. Generate coverage files. sbatch_bedtoolscoverage.sh
13. Generate count files. sbatch_processcovfiles.sh
14. Generate data tables for each annotation feature type. sbatch_processcounts.sh