Hi,

I tried spliceR to identify differential AS event between 2 conditions.  I followed the example script from spliceR document:

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# A) Retrieve data from Cufflinks

cuffDB <- readCufflinks(dir='./cuffdiff_output/', rebuild=TRUE, gtfFile=‘./cuff-

merge/merged.gtf’) # create SQL database via cummeRbund

mySpliceRList <- prepareCuff(cuffDB) # Extract data from SQL database

# B) Identify ORFs and annotate PTCs in transcripts

require("BSgenome.Hsapiens.UCSC.hg19",character.only = TRUE) # load genome sequence

ucscCDS <- getCDS(selectedGenome="hg19", repoName="UCSC") # Get annotated ORFs

mySpliceRList <- annotatePTC(mySpliceRList, ucscCDS, Hsapiens) # Analyze ORFs

# C) Analyze alternative splicing in transcripts

mySpliceRList <- spliceR(mySpliceRList, compareTo='preTranscript', filters= 'isoOK')

# D) Create GTF file

generateGTF(mySpliceRList, filters="isoOK", filePrefix=’./outputPaht/outputName’)

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What is strange is in my output file, some of the genes were reported to have significant isoform expression, but not particular AS type associated, below is an example:

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    seqnames   start     end width strand spliceR.isoform_id spliceR.sample_1 spliceR.sample_2 spliceR.gene_id spliceR.CDS_id spliceR.gene_short_name spliceR.TSS_group_id spliceR.class_code
148     chr1 8021713 8045342 23630      *     TCONS_00000148          control            dose1     XLOC_000066             NA                   PARK7                TSS83                  =
    spliceR.nearest_ref_id spliceR.length spliceR.coverage spliceR.seqnames spliceR.strand spliceR.source spliceR.type spliceR.score spliceR.phase spliceR.gene_name spliceR.oId spliceR.nearest_ref
148              NM_007262            961               NA             chr1              *      Cufflinks         exon            NA            NA             PARK7   NM_007262           NM_007262
    spliceR.contained_in spliceR.gene_status spliceR.gene_value_1 spliceR.gene_value_2 spliceR.gene_log2_fold_change spliceR.gene_p_value spliceR.gene_q_value spliceR.gene_significant
148                 <NA>                  OK              250.315              315.129                      0.332198              0.00045           0.00137226                      yes
    spliceR.iso_status spliceR.iso_value_1 spliceR.iso_value_2 spliceR.iso_log2_fold_change spliceR.iso_p_value spliceR.iso_q_value spliceR.iso_significant spliceR.cdsPosGenomic
148                 OK             184.003             237.155                     0.366099             0.00105          0.00501938                     yes               8022846
    spliceR.stopPosGenomic spliceR.ExonWithStart spliceR.ExonWithStop spliceR.cdsPosTranscipt spliceR.stopPosTranscipt spliceR.stopDistance spliceR.junctionIndex spliceR.PTC spliceR.major
148                8045113                     2                    7                     164                      733                 -161                     0       FALSE            NA
    spliceR.IF1 spliceR.IF2 spliceR.dIF spliceR.ESI spliceR.MEE spliceR.MESI spliceR.ISI spliceR.A5 spliceR.A3 spliceR.ATSS spliceR.ATTS spliceR.analyzed spliceR.ESI.start spliceR.ESI.end
148     73.5086     75.2565      1.7479           0           0            0           0          0          0            0            0              yes              <NA>            <NA>
    spliceR.MEE.start spliceR.MEE.end spliceR.MESI.start spliceR.MESI.end spliceR.ISI.start spliceR.ISI.end spliceR.A5.start spliceR.A5.end spliceR.A3.start spliceR.A3.end spliceR.ATSS.start
148              <NA>            <NA>               <NA>             <NA>              <NA>            <NA>             <NA>           <NA>             <NA>           <NA>               <NA>
    spliceR.ATSS.end spliceR.ATTS.start spliceR.ATTS.end
148             <NA>               <NA>             <NA>

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Did I do anything wrong?  How should I interpret the results?

Thank you very much for your help.

You should interpret the result as the isoforms you find to be significant contains all the exoninformation from that gene (meaning that the isoforms only contain a subset of these exons).