Converter to support differential AS analysis tools



Converter basic usage


ASpedia supports to retrieve multiple AS IDs. BED format input file is required and specific column and formatted AS ID is mandatory. Please read manual about input file. BED input file could be generated from RNA-Seq analysis results. For the user convenience, we provide format conversion tool for specific applications. Currently results generated by rMATS and MISO could be converted using our util.

Our execution file is OS-independent, and requires JRE 1.6 version.

  • Download jar file

  • Options

    -i/--input Input directory or file name (required)
     
    -o/--output Output file name (required)
     
    -p/--program Differential AS event analysis program to create result (required)
    Value: rMATS or MISO
     
    -a/--AS_type Input file's AS type, when use single file or MISO's result converting (required)
    Value: A3SS, A5SS, SE, MXE, or RI

  • Examples


    java -jar DASEResultConvertor.jar -i rMATS_result_dir -o output_file_name -p rMATS
    java -jar DASEResultConvertor.jar -i rMATS_A3SS_result_file -o output_file_name -p rMATS -a A3SS

    java -jar DASEResultConvertor.jar -i MISO_result_dir -o output_file_name -p MISO -a A3SS
    java -jar DASEResultConvertor.jar -i MISO_A3SS_result_file -o output_file_name -p MISO -a A3SS





  • Data process workflow for differential AS analysis


    1. Differential alternative splicing analysis


    1) rMATS analysis method


    rMATS analyzes alternative splicing events; skipped exon (SE), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), and retained intron (RI). Possible alternative splicing events are identified from the RNA-Seq data and annotation of transcripts in GTF format. All output files are in your specified output directory. For alternative splicing annotation, you can use MATS_output folder or “AS_Event.MATS.JunctionCounts.txt” files. More information about output files is available http://rnaseq-mats.sourceforge.net/user_guide.htm

    1-1) rMATS example



    $python RNASeq-MATS.py –b1 SF3B1_mut.bam –b2 SF3B1_wt.bam –gtf hg19_gen_annot.gtf \
    –o SF3B1wt_vs_mut –t paired –len 50



    Note that the output directory structure is:

    SF3B1wt_vs_mut
    ├----- ASEvents
    ├----- MATS_output
    |      |------ A3SS.MATS.JunctionCountOnly.txt
    |      ├------ A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
    |      └------ ...
    ├----- summary.txt
    ├----- ASEvents/
    ├----- SAMPLE_1/
    ├----- SAMPLE_2/
    ├----- commands.txt
    └----- log.RNASeq-MATS


    Now run converter.jar (Go on 2. Running converter tool for alternative splicing annotation)

    2. Running converter tool to prepare ASpedia input file


    To identify alternative splicing event annotation, you should upload the alternative splicing lists of bed format. For user convenience, we provide a tool converting to bed format from analysis result file using rMATS and MISO. We are not require ‘chr’ prefix in chromosome naming, namely you can use either ‘chr1’ or ‘1’. But our converter tool provides the chromosome name with ‘chr’ prefix .

    1) First, Download the jar file (DASEResultConvertor.jar) in UTIL page

    2) Input requirements

    2-1) rMATS

    - Output directory (eg. MATS_output folder) or
    - Each AS_event files (eg. A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt)

    2-2) MISO

    - The summarizing output files with the Bayes factors with each AS_event (eg. *.miso_bf)

    3) Examples

    To convert your result file, use the following command line each used tool:

    3-1) rMATS example



    $java –jar DASEResultConvertor.jar -i SF3B1wt_vs_mut/MATS_output/ \
          -o SF3B1wt_vs_mut.aspedia.bed \
          -p rMATS
    # or
    $java –jar DASEResultConvertor.jar -i A3SS.MATS.ReadsOnTargetAndJunctionCounts \
          -o A3SS_SF3B1wt_vs_mut.aspedia.bed \
          -p rMATS -a A3SS


    While your job processed, you can check your job status and your data type as below:

    CONVERTING STATUS: starting file conversion using SF3B1wt_vs_mut/MATS_output//A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
    CONVERTING STATUS: starting file conversion using SF3B1wt_vs_mut/MATS_output//A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
    CONVERTING STATUS: starting file conversion using SF3B1wt_vs_mut/MATS_output//MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
    CONVERTING STATUS: starting file conversion using SF3B1wt_vs_mut/MATS_output//SE.MATS.ReadsOnTargetAndJunctionCounts.txt
    CONVERTING STATUS: starting file conversion using SF3B1wt_vs_mut/MATS_output//RI.MATS.ReadsOnTargetAndJunctionCounts.txt
    ***FINAL REPORT***
    Finally total 219151 ASEs were converted from your input.
    The output file includes 19132 A5SS, 38721 A3SS, 37998MXE, 116164 SE, and 7136 RI events.


    3-2) MISO example


    $java –jar DASEResultConvertor.jar -i SF3B1wt_vs_mut/SF3B1wt_vs_mut.A3SS \
    -o A3SS_SF3B1wt_vs_mut.aspedia.bed \
    -p MISO –a A3SS
    # or
    $java –jar DASEResultConvertor.jar \
    -i SF3B1wt_vs_mut/SF3B1wt_vs_mut.A3SS/bayes-factors/SF3B1wt_vs_mut.A3SS.miso_bf \
    -o A3SS_SF3B1wt_vs_mut.aspedia.bed \
    -p MISO –a A3SS


    While your job processed, you can check your job status and your data type as below:

    CONVERTING STATUS: starting file conversion using
    SF3B1wt_vs_mut/MATS_output/SF3B1wt_vs_mut.A3SS/bayes-factors/SF3B1wt_vs_mut.A3SS.miso_bf
    ***FINAL REPORT***
    Finally total 38701 ASEs were converted from your input.
    The output file includes 38701 A3SS events.


    4) Converted ASpedia BED format

    The specification of ASpedia BED format is described in HELP page.
    If you follow the format and AS ID rule, user could query other differential AS analysis result in ASpedia.

    3. Searching alternative splicing event annotation

    For searching alternative splicing event annotation, you should upload bed formatted file with alternative splicing lists obtained from convertor tool.
    Once you have uploaded the AS lists, you could get results on website or e-mail.

    3-1) Getting results from website

    To just get results from website, select ‘in screen’ from the drop-down lists and click on the Search (in Gene symbol search mode) or Submit button. And then you can check status and results with annotated AS lists of your input
    (If you uploaded your AS lists as attached file, check your input search status and click on View summary button as below).



    3-2) Getting results via e-mail

    We offer to receive your results by e-mail. To get results via e-mail, select ‘e-mail’ from the drop-down lists and enter your e-mail address in the Email box.


    Now, the page for notifications will be displayed as shown below and you will receive e-mail in a few minutes when the download of the result reports with annotating the AS lists you uploaded is available .