shao-group / rnabridge-align

rnabridge-align is an efficient tool to bridge paired-end RNA-seq reads

Overview

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.

Release

Latest release of rnabridge-align is v1.0.1.

Installation

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.

Download Boost

If Boost has not been downloaded/installed, download Boost (license) from (http://www.boost.org). Uncompress it somewhere (compiling and installing are not necessary).

Install htslib

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

Compile rnabridge-align

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.

Usage

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.

rnabridge-align's Issues

Feature request?

Hello,

This is a great tool and exactly what I was looking for, however I was wondering if it was possible to only perform bridging or partitioning based on the read tag? I'm specifically trying to bridge single cell data and would like to only bridge reads by barcodes. Would this be easy to add?
The other solution on my end was to have a wrapper script that fed in split bams based on my barcodes but this is rather inefficient as you might imagine.

Thanks,
Chang