mzytnicki / get_unmapped

Find reads not mapped by srnaMapper

get_unmapped

Find reads not mapped by srnaMapper.

Get the code

Using git:

git clone https://github.com/mzytnicki/get_unmapped.git
cd get_unmapped

Or download via link https://github.com/mzytnicki/get_unmapped/archive/refs/heads/main.zip and uncompress.

Compile the code

On Linux, type

g++ -O2 get_unmapped.cpp -o get_unmapped

(This should work with Clang too). You should have the get_unmapped executable.

Use get_unmapped

We suppose that you have the fastq file file.fastq, that you mapped with srnaMapper (or any other tool), in order to have file.sam.

In this case, you can type:

get_unmapped file.sam file.fastq > file_unmapped.fastq

Using bash, you can still use a BAM file, and a compressed FASTQ file, using the following command:

./get_unmapped <( samtools view file.bam ) <( zcat file.fastq.gz ) > file_unmapped.fastq

What get_unmapped does

This tools only retrieves the FASTQ sequences that are not present in the SAM file.

Specifically, if a read can be mapped several times, srnaMapper will output this read, but it will flag it as unmapped. This tool, get_unmapped, will not retrieve these reads.