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Source Added scripts and results_overview Nov 20, 2014
README.md added link to the example data Feb 20, 2015

README.md

SplicePie

A pipeline to analyze non-sequential and multi-step splicing

SplicePie contains three major analysis steps: analyzing the order of splicing per sample, looking for recursive splicing events per sample and summarizing predicted recursive splicing events for all analyzed sample (it is recommended to use more samples for higher reliability). The first two steps are performed individually on each sample and the last step looks at the overlap in all samples. However, the analysis can be run on one sample as well.

All scripts and commands are called from a single run.sh script. You have to create it yourself from run_template.sh (please go to the USAGE section for more details). Before running run.sh you have to specify the locations of the scripts and the input files within it (please check the USAGE section for more details).

The pipeline is designed to analyze captured RNA-Seq data, however, in principle it could be run on any RNA-Seq dataset. Please keep in mind that coverage is essential and especially the coverage of introns will largely influence the reliability of the predictions.

Requirements

You have to install the following packages:

  1. samtools
  2. piletools
  3. wiggelen
  4. R

You also need to have the following [scripts] (https://git.lumc.nl/i.pulyakhina/pipeline_paper/blob/master/Source/Scripts.tar.gz) on your computer: download the archive containing the scripts and extract the scripts to your folder of preference:

mkdir folder/of/preference
tar xzf -C folder/of/preference scripts.tar.gz

Input files

You can first have a look at the example input files and use them in your test run of the pipeline. Download the archive with the example text data files and extract the files to yur folder of preference:

tar xzf -C folder/of/preference data.tar.gz

You will have to specify the full path both to the scripts and to the files when running the pipeline. You do not have to do it manually, if you placed all scripts in one location and all data files in one location, you can run the following commands on run_template.sh to create a new run.sh script that will contain full pathes to your data files and scripts. The only thing that you still need to specify manually is the full path to your reference sequence:

cat run_template.sh | sed 's/PATH_TO_SCRIPTS/path_to_the_folder_with_scripts/g' | sed 's/PATH_TO_DATA/path_to_the_folder_with_data/g' > run.sh

If you want to start directly with the analysis of your own data, or you want to know more about the exmaple data, here is a brief explanation of every file:

  • example_annotation.bed: an annotation file of your gene of interest in a GTF format
  • example_alignment1.bam: a bam file of sample 1 containing reads mapped to the region of interest
  • example_alignment2.bam: a bam file of sample 2 containing reads mapped to the region of interest
  • example_alignment1.bam.bai: an index of example_alignment1.bam
  • example_alignment2.bam.bai: an index of example_alignment2.bam
  • example_region.bed: a bed file containing regions to be excluded (using bedtools you can exclude/include certain regions, such as promoters, pseudogenes, UTRs, etc.

Usage

In order to run the pipeline you need to execute run.sh, however, some pre-processing steps are required.

You have to specify the full pathes to the SCRIPTS that you just downloaded to your folder of preference.

Please make sure that you sepcify the full path:

  • CLASSIFICATION="/folder/of/preference/class_plus.pl"
  • MAPPED_READS="/folder/of/preference/mapped_reads_from_sam_file.pl"
  • SSI_SCRIPT="/folder/of/preference/ssi.pl"
  • ZERO_TO_WIG="/folder/of/preference/add_zero_to_wig.pl"
  • AVERAGE_WIG_COV="/folder/of/preference/wig_average_exonic_coverage.pl"
  • WIG_COV_CHANGE="/folder/of/preference/wig_change_cov.pl"
  • R_PROCESS="/folder/of/preference/process_SSI.R"
  • MED_COV_PROBES="/folder/of/preference/med_cov_per_region.pl"
  • SAM_READS_FROM_REGION="/folder/of/preference/get_sam_reads_within_region.pl"
  • GET_EXEX_READS_PER_INTRON="/folder/of/preference/get_exex_i_PER_INTRON_reads_from_sam.pl"
  • GET_EXEX_READS_PER_JUNCTION="/folder/of/preference/get_exex_i_PER_JUNCTION_from_sam.pl"
  • REMOVE_EX_EX="/folder/of/preference/remove_exex_from_sam.pl"
  • PARSE_ANN="/folder/of/preference/parse_annotation_gtf2txt.pl"
  • GET_SPLIT_READ_FOR_WIG="/folder/of/preference/get_split_reads_for_wigg.pl"
  • RECURS_MATRIX="/folder/of/preference/recursive_splicing_matrix.pl"
  • PARSE_RECURS_OUTPUT="/folder/of/preference/parse_recursive_output.pl"
  • WIG_PEAKS="/folder/of/preference/wig_peaks_sign.pl"

You also need to specify the full pathes to the following input files:

  1. ANNOTATION="/folder/of/interest/example_annotation.txt"

  2. CUTOFF_COV="5000"

This is the cutoff of the coverage to normalize the wiggle files. Wiggle file with the total gene coverage will be scaled and the average coverage will equal CUTOFF_COV.

  1. PROBES_TO_INCLUDE="/folder/of/preference/example_region.bed"

  2. REFSEQ="/full/path/to/the/reference.fa"

Full path to the reference sequence that was used to generate the alignment. Here we do not provide the reference sequence for the sake of space. For our example alignments we used Homo Sapiens reference of build hg19.


When everything listed above is specified in your run.sh file, you can run it.

chmod 755 run.sh
./run.sh input_1.bam input_2.bam ...

All bam files should be indexed (and a bam.bai files should be placed in the same folder).

In order to verify that the pipeline works properly on your machine, please check the [list] (LINK) of the names and the sizes of the results files.

About

This pipeline was developed by Irina Pulyakhina (i.pulyakhina@lumc.nl), Jeroen Laros (j.f.j.laros@lumc.nl) and Peter-Bram 't Hoen (p.a.c._t_hoen@lumc.nl) with the help of Martijn Vermaat and Michel Villerius.