Exercise 4a

a) Fetch all transcript variations (germline and somatic) in transcript ENST00000001008 in human and retrieve the following information:

  • Variation name
  • Consequence type (most severe)
  • Amino acid change*
  • Position in cDNA* and position in translation*

b) In a second attempt filter for transcript variations of consequence type: ‘missense_variant’

Hintfetch_all_by_Transcripts method requires a listref of objects; so use e.g. [$transcript] instead of $transcript

* if information exists


AnswerAnja explains the answers to these questions in this 4 min video. You can also download her sample script and expected output.