Half-Life Estimation in a Batch (HLEB)

Repository contains an array of scripts and tools to count base conversion rates from bam files obtained from a Slamseq run.

Default approach

To run the whole pipeline, one needs to execute Master.sh script. Run bash Master.sh --help to get an overview of the available options and arguments. The standard approach would be:

 git clone https://github.com/melonheader/HLEB.git
 cd HLEB
 bash Master.sh \
    -i <path_to_bam_files> (wild cards are accepted) \
    -o <output_path> \
    -g <genome_to_use> \
    -a <genome_annotation_to_use> \
    -e <name_of_the_run> \
    -n <numer_of_cores>

Genome annotation

Repository contains a helper script to flatten the GTF annotation for the pipeline. To do so, run:

 bash collapse_gtf.sh \
    <path_to_gtf> \
    <exon|three_prime_utr> \
    <path_to_write_result>

Currently, paths to the genome and annotation are hardcoded. To use this in a fresh installation one needs to change paths on lines 140-142 in Master.sh. Easiest appraoch would be to create a directory with self-explanatory name for a genome of choice. Then, create a subdirectory called slam_annot inside. There, put a genome fasta under the name of genome_fasta.fa. Finally, put to the same folder an output of bash collapse_gtf.sh that was generated from the GTF annotation of the same genome.

To keep in mind

User needs to provide a path to Varscan binary for SNP quantification. Currently, this can be done by changing the path of the argument -v on the line number 168 in Master.sh.