1. Anduril Avatar Anduril
  2. Anduril
  3. sequencing
  4. Issues

Align function is old

Issue #13 resolved
Former user created an issue

The Align function in anduril2 is an old version of the Align function in anduril1. In particular the current anduril2 version does not support STAR. Update need to be done fast.

Comments (5)

  3. Lilli Saarinen

    Bowtie and Bowtie2 are working with test cases 5, 6, 7, 8.

    TODO: TopHat needs to be fixed and STAR is missing.

    Check: ssh://hg.anduril.org//opt/hg/personal/cerverat/QCFasta align.scala, testCases, test.scala

  4. Alejandra Cervera

    Current version is using the old way of calling picard (in separate jars for each, not just picard.jar) which is throwing an error ... Tophat can be deprecated, no need to include it Star may be included since STAR component runs only one sample at a time, STAR in align function used to accept all samples together, and also multiple files per sample,and STAR 2 pass function runs star twice, so it coud be added or not .... The question is it worth it to keep Align function for bwa and bowtie or should we include more aligners or scrap the whole thing?

  6. Log in to comment
Assignee
Type
bug
Priority
major
Status
resolved
Votes
0
Watchers
2
Jira: the preferred issue tracker for Bitbucket. Join the team!