Tyrev / MapSplice

Bioinformatics software release from Jinze Liu's Bioinformatics lab @ UKy

MapSplice3

MapSplice3 is an spliced aligner. It maps RNA-seq onto reference genome, and can be used to detect splice junctions, gene fusions, and circular RNAs.

System Requirements

MapSplice3 has been tested on Linux platforms with the following system settings.

• Red Hat 4.4.5-6
• gcc version 4.9.1

Manual

There are two subfolders in the package: "indexing" and "mapping".

Code in subfolder "indexing" is used to build index. Code in subfolder "mapping" is used to perform the spliced alignment.

How to run MapSplice3?

1. Build index for MapSplice3.

Note: before building index, you need to put all the sequence files of reference genome into a directory (like /PATH/hg19/). And all the sequence files are required to be in the following format:

(1) In "FASTA" format, with ".fa" extension. (2) One chromosome per sequence file. (3) Chromosome name in the header line (">" not included) is the same as the sequence file base name, and does not contain any blank space. E.g. If the header line is ">chr1", then the sequence file name should be "chr1.fa". (5) No other files in the same folder.

Installation:

Go to directory "indexing", and run "make buildIndex".

Running:

Command Line:

./buildIndex <path-to-chromosomes-folder> <path-to-index-folder>

Example:

./buildIndex /PATH/hg19/ /PATH/index/

2. Map reads onto reference genome and detect co-linear splice junctions, back-splice junctions (circular RNA), and gene fusions.

Installation:

Go to directory "mapping", and run "make mps".

Running: There are four modes in total. All the parameters are required for each mode.

i). map co-linear transcript reads only to detect co-linear splice junctions

Command Line:

bin/mps_regular -G <path-to-index> -1 <read-end1> -2 <read-end2> -T <threads-num> -O <output-folder>

Example:

bin/mps_regular -G /PATH/index/ -1 /PATH/read_end1.fa -2 /PATH/read_end2.fa -T 16 -O /PATH/mps3_results/

ii). map co-linear transcript and circualr RNA reads to detect both co-linear splice junctions and back-splice junctions

Command Line:

bin/mps_regular_circRNA -G <path-to-index> -1 <read-end1> -2 <read-end2> -T <threads-num> -O <output-folder>

Example:

bin/mps_regular_circRNA -G /PATH/index/ -1 /PATH/read_end1.fa -2 /PATH/read_end2.fa -T 16 -O /PATH/mps3_results/

iii). map co-linear transcript and gene fusion reads to detect co-linear splice junctions and gene fusions

Command Line:

# Step 1
bin/mps_regular_fusion -G <path-to-index> -1 <read-end1> -2 <read-end2> -T <threads-num> -O <output-folder> --fusion-post-gene-ann <path-to-gene-annotation-file> --fusion-post-paralog-gene <path-to-paralog-gene-file>

# Step 2
bin/mps3_fusion_post_new \
<path-to-index> \
<output-folder-step1> \
<path-to-gene-annotation-file> \
<threads-num> \
<fusion-junc-read-support-min> \
<path-to-paralog-gene-file> \
<output-folder>

Example:

# Step 1
bin/mps_regular_fusion -G /PATH/index/ -1 /PATH/read_end1.fa -2 /PATH/read_end2.fa -T 16 -O /PATH/mps3_results/ --fusion-post-gene-ann /PATH/gene_annotation --fusion-post-paralog-gene /PATH/paralog_gene_file

# Step 2
bin/mps3_fusion_post_new \
/PATH/index/ \
/PATH/step1_results/ \
/PATH/gene_annotation \
16 \
5 \
/PATH/paralog_gene_file \
/PATH/fusion_post_output/

iv). map co-linear transcript, circualr RNA and gene fusion reads to detect co-linear splice junctions, back-splice junctions, and gene fusions

Command Line:

# Step 1
bin/mps_regular_circRNA_fusion -G <path-to-index> -1 <read-end1> -2 <read-end2> -T <threads-num> -O <output-folder> --fusion-post-gene-ann <path-to-gene-annotation-file> --fusion-post-paralog-gene <path-to-paralog-gene-file>

# Step 2
bin/mps3_fusion_post_new \
<path-to-index> \
<output-folder-step1> \
<path-to-gene-annotation-file> \
<threads-num> \
<fusion-junc-read-support-min> \
<path-to-paralog-gene-file> \
<output-folder>

Example:

# Step 1
bin/mps_regular_circRNA_fusion -G /PATH/index/ -1 /PATH/read_end1.fa -2 /PATH/read_end2.fa -T 16 -O /PATH/mps3_results/ --fusion-post-gene-ann /PATH/gene_annotation --fusion-post-paralog-gene /PATH/paralog_gene_file

# Step 2
bin/mps3_fusion_post_new \
/PATH/index/ \
/PATH/step1_results/ \
/PATH/gene_annotation \
16 \
5 \
/PATH/paralog_gene_file \
/PATH/fusion_post_output/

example files for gene annotation and paralog gene can be found in:

gene annotation file: https://drive.google.com/file/d/1J8fVELkXqtiAz_AYQoco22kVQoJlSWnt/view?usp=sharing

paralog gene file: https://drive.google.com/file/d/1bp1N5W7Rdn6A-mk8DGCFJaHamaVJcOd8/view?usp=sharing

Users can also prepare and provide their own gtf and paralog gene files using the same format as in those example files.

License

Please refer to LICENSE.txt