Contact: [email protected]
- To install, simply do as "root":
- $ cd rnainigo/ $ python setup.py install
Usage: $ aluline --reference <humrep.ref> <humsub.ref> --ThreadsN <number of threads> --reads <read1.fq> [read2.fq] --outdir [output directory]
- Some parameters required to have the program work:
--reference Path to reference sequences: ALU and L1HS --reads Path to your short reads, in FASTQ format - Optional parameter:
--ThreadsN max Threads For parallel computing in BWA alignment process --outdir Output directory
Example:
- For human:
- $ aluline --reference rnainigo/lib/ref.fa --ThreadsN 32 --reads read1.fq.gz read2.fq.gz --outdir output
- For mouse:
- $ aluline --reference rnainigo/lib/mousub.ref --ThreadsN 32 --reads read1.fq.gz read2.fq.gz --outdir output