Install

Manual install

• Download the tool with git clone --recurse-submodules https://github.com/mzytnicki/srnaMapper.git
• Go the directory with cd srnaMapper
• Compile with make

You should have the zlib library, and a C++11 compiler.

With bioconda

If you have bioconda ready, you can install srnaMapper with:

conda install -c bioconda srnamapper

Generating the genome index

srnaMapper uses the bwa API, and the bwa index files. Use bwa index to generate the index files.

Note

As in bwa, ambiguous nucleotides in the genome are converted to a random nucleotide.

The procedure is identical for the reads.

Using srnaMapper

Once compiled type ./srnaMapper parameters.

Compulsory parameters:

• -r string: file name in FASTQ format
• -g string: prefix of the genome database (produced by bwa build)
• -o string: output file in SAM format

Optional parameters:

• -e int: maximum number of errors (default: 2)
• -t int: number of threads (default: 1)
• -n int: discard reads when they map more than n times (default: 5)
• -f int: low complexity threshold, more is more lenient (default: 6)
• -u: if set, print all the mapped reads in a unique SAM file (with the counts for each sample)
• -s int: set the random seed (time otherwise)
• -h: the help message

Notes:

• The -r option should be repeated once per input file.
• Unless the the -u option is set, the -o option should also be repeated once per input file.

Example:

./srnaMapper -r cond1_rep1.fastq -r cond1_rep2.fastq -r cond2_rep1.fastq -r cond2_rep2.fastq -g genome -o cond1_rep1.sam -o cond1_rep2.sam -o cond2_rep1.sam -o cond2_rep2.sam -t 10