rnabridge-align implements an efficient algorithm to bridge paire-end RNA-seq reads, i.e., to determine the alignment of full fragments given the alignment of two mate ends. Its sister tool, rnabridge-denovo, determines the sequences of full fragments given the sequences of paired-end reads. See rnabridge-test for the evaluation of both tools.
Latest release of rnabridge-align is v1.0.1.
Download the source code of rnabridge-align from
here.
rnabridge-align uses additional libraries of Boost and htslib.
If they have not been installed in your system, you first
need to download and install them. You might also need to
export the runtime library path to certain environmental
variable (for example, LD_LIBRARY_PATH, for most linux distributions).
After install these dependencies, you then compile the source code of rnabridge-align.
If some of the above dependencies are not installed to the default system
directories (for example, /usr/local, for most linux distributions),
their corresponding installing paths should be specified to configure of rnabridge-align.
If Boost has not been downloaded/installed, download Boost (license) from (http://www.boost.org). Uncompress it somewhere (compiling and installing are not necessary).
If htslib has not been installed, download htslib (license) from (http://www.htslib.org/) with version 1.5 or higher. (Note that htslib relies on zlib. So if zlib has not been installed in your system, you need to install zlib first.)
Use the following commands to build htslib:
./configure --disable-bz2 --disable-lzma --disable-gcs --disable-s3 --enable-libcurl=no
make
make install
The default installation location of htslib is /usr/lib.
If you would install it to a different location, replace the above configure line with
the following (by adding --prefix=/path/to/your/htslib to the end):
./configure --disable-bz2 --disable-lzma --disable-gcs --disable-s3 --enable-libcurl=no --prefix=/path/to/your/htslib
In this case, you also need to export the runtime library path (note that there
is an additional lib following the installation path):
export LD_LIBRARY_PATH=/path/to/your/htslib/lib:$LD_LIBRARY_PATH
Use the following to compile rnabridge-align:
./configure --with-htslib=/path/to/your/htslib --with-boost=/path/to/your/boost
make
If some of the dependencies are installed in the default system directory (for example, /usr/lib),
then the corresponding --with- option might not be necessary.
The executable file rnabridge-align will appear at src/rnabridge-align.
The usage of rnabridge-align is:
./rnabridge-align -i <input.bam> -o <output.bam> [-r reference.gtf] [options]
The input.bam is the read alignment file generated by some RNA-seq aligner, (for example, TopHat2, STAR, or HISAT2).
Make sure that it is sorted; otherwise run samtools to sort it:
samtools sort input.bam > input.sort.bam
The alignment of entire fragments shall be written to output.bam.
rnabridge-align also supports making use the reference transcriptome to improve bridging accuracy.
The reference transcriptome can be provided with -r reference.gtf.
rnabridge-align support the following parameters.
| Parameters | Default Value | Description |
|---|---|---|
| --help | print usage of rnabridge-align and exit | |
| --version | print version of rnabridge-align and exit | |
| --preview | show the inferred library_type and fragment-length-range and exit |
|
| --library_type | empty | chosen from {empty, unstranded, first, second} (see below) |
| --min_bridging_score | 0.5 | the minimized bottleneck weight in bridging path |
| --dp_solution_size | 10 | candidate number of bridgign paths |
| --dp_stack_size | 5 | number of weights maintained for each bridging path |
| --max_clustring_flank | 30 | maximized basepair difference for being in an equivalent class |
| --flank_tiny_length | 10 | maximized length for reconsidering error correction |
| --flank_tiny_ratio | 0.4 | maximized ratio for reconsidering error correction |
| --min_splice_bundary_hits | 1 | the minimum number of spliced reads required to support a junction |
| --max_num_cigar | 1000 | ignore reads with CIGAR size larger than this value |
--library_type is highly recommended to provide. The unstranded, first, and second
correspond to fr-unstranded, fr-firststrand, and fr-secondstrand used in standard Illumina
sequencing libraries. If none of them is given, i.e., it is empty by default, then rnabridge-align
will try to infer the library_type by itself (see --preview). Notice that such inference is based
on the XS tag stored in the input bam file. If the input bam file do not contain XS tag,
then it is essential to provide the library_type to rnabridge-align. You can try --preview to see
the inferred library_type.