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plotBambu counts not explained #492

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plotBambu counts not explained#492

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@stfacc
stfacc
opened on Jun 10, 2025

plotBambu seems to use "count" values for transcript usage, different from all of the following:

  • counts_transcript.txt
  • CPM_transcript.txt
  • fullLengthCounts_transcript.txt
  • uniqueCounts_transcript.txt

Please explain the discrepancy in the documentation

Activity

  1. stfacc
    changed the title [-]plotBambu counts not labelled[/-] [+]plotBambu counts not explained[/+] on Jun 10, 2025

  2. cying111 commented on Jun 13, 2025

    @cying111
    cying111
    on Jun 13, 2025
    Collaborator

    Hi @stfacc ,

    Just to clarify, the counts shown in plotBambu are log2 normalized CPM values for transcript expression.
    Hope this helps answer your question.

    Thanks and best regards
    Ying

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