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.
MapSplice3 has been tested on Linux platforms with the following system settings.
- Red Hat 4.4.5-6
- gcc version 4.9.1
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?
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.
Go to directory "indexing", and run "make buildIndex".
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.
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/
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.
Please refer to LICENSE.txt
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