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  1. Barna Package
  2. BARNA-394

Astalavista Scorer does not output splice site type in v4.0

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: AStalavista 4.0 (API 1.30)
    • Fix Version/s: None
    • Component/s: Astalavista
    • Labels:
      None

      Description

      In Astalavista 4.0 the Scorer tool no longer includes information about the splice site type in the output VCL file (e.g. TYPE=U2_GTAG). It only includes the mode (MOD=CON or MOD=ALT).

      In Astalavista 3.2 (API 1.22) it did include the "TYPE=" field in the output VCL.

      Example output (splice sites are the same in both VCLs):

      Astalavista 3.2 VCL:
      3R 835491 835491^3R ATATGTATCCTTA . 5.590205 PASS TYPE=U12_GTAG;MOD=CON;
      3R 869486 869486-3R GGTCGTTCTATATTTAAACCCAATAGACTTA . -Infinity q-1000 TYPE=UNKNOWN;MOD=CON;
      3R 869548 869548^3R TAAGGTAAGCTTA . 5.725247 PASS TYPE=U2_GTAG;MOD=CON;
      3R 895786 895786-3R TTGACCTTTATAATTTAAAATTTCAGCAAAC . -Infinity q-1000 TYPE=UNKNOWN;MOD=CON;

      Astalavista 4.0 VCL:
      3R 835491 835491^3R ATGTATCCTT . -20002.342 q-1000 MOD=CON;
      3R 869486 869486-3R GTCGTTCTATATTTAAACCCAATAGACT . 3.4419343 PASS MOD=CON;
      3R 869548 869548^3R AGGTAAGCTT . -10003.402 q-1000 MOD=CON;
      3R 895786 895786-3R TGACCTTTATAATTTAAAATTTCAGCAA . 3.1529703 PASS MOD=CON;

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            Assignee:
            micha Micha Sammeth
            Reporter:
            martin Martin Oti
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              Dates

              Created:
              Updated: