Changeset 5773 for trunk/config


Ignore:
Timestamp:
Sep 29, 2011, 3:14:56 PM (11 years ago)
Author:
Nicklas Nordborg
Message:

References #1152: Handling short read transcript sequence data

  • Adds a 'Cufflinks' raw data type with five columns: coverage, fpkm, fpkm_lo, fpkm_hi and status
  • Define FPKM_TRACKING file type and MIME type.
  • Adds left(string, index) as a JEP formula so that we can parse out the chromosome from the 'locus' column in the tracking files.
  • Define two new configurations for the raw data importer that parses cufflinks isoform files.
File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/config/dist/raw-data-types.xml

    r4888 r5773  
    35363536    </intensity-formula>
    35373537  </raw-data-type>
     3538  <raw-data-type
     3539    id="cufflinks"
     3540    channels="1"
     3541    name="Cufflinks"
     3542    table="RawDataCufflinks"
     3543    description="Cufflinks isoforms/gene-level expression values in FPKM tracking format">
     3544    <property
     3545      name="coverage"
     3546      title="Coverage"
     3547      description="Estimate for the absolute depth of read coverage across the object."
     3548      column="coverage"
     3549      type="float"
     3550      averagemethod="arithmetic_mean"
     3551    />
     3552    <property
     3553      name="fpkm"
     3554      title="FPKM"
     3555      description="Fragments Per Kilobase of exon per Million fragments mapped."
     3556      column="fpkm"
     3557      type="float"
     3558      averagemethod="geometric_mean"
     3559    />
     3560    <property
     3561      name="fpkm_lo"
     3562      title="FPKM lo"
     3563      description="The lower bound of the 95% confidence interval on the FPKM."
     3564      column="fpkm_lo"
     3565      type="float"
     3566      averagemethod="geometric_mean"
     3567    />
     3568    <property
     3569      name="fpkm_hi"
     3570      title="FPKM hi"
     3571      description="The upper bound of the 95% confidence interval on the FPKM."
     3572      column="fpkm_hi"
     3573      type="float"
     3574      averagemethod="geometric_mean"
     3575    />
     3576    <property
     3577      name="status"
     3578      title="Status"
     3579      description="Quantification status. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution."
     3580      column="status"
     3581      type="string"
     3582      length="255"
     3583      averagemethod="none"
     3584    />
     3585    <intensity-formula
     3586      name="fpkm"
     3587      title="FPKM"
     3588      description="Fragments Per Kilobase of exon per Million fragments mapped."
     3589      >
     3590      <formula
     3591        channel="1"
     3592        expression="raw('fpkm')"
     3593      />
     3594    </intensity-formula>
     3595 
     3596  </raw-data-type>
    35383597</raw-data-types>
    35393598
Note: See TracChangeset for help on using the changeset viewer.