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Possible reasons, solutions for the'invalid times argument' error (Plot ribosome pr.)
06-Aug-2015, 09:32 AM (This post was last modified: 06-Aug-2015 11:30 AM by vimalkumarvelayudhan.)
Post: #1
Information Possible reasons, solutions for the'invalid times argument' error (Plot ribosome pr.)
Possible reasons and solutions for the "invalid times argument" error when using
the Plot Ribosome Profile tool (RiboSeq -> riboSeqR analysis)

When attempting to plot the ribosome profile of a transcript, you might get an
error message like the following:

...
rpy2.rinterface.RRuntimeError: Error in rep(0, ceiling(transceiling/3) * 3) : invalid 'times' argument


Possible reasons and solutions:

  1. An incorrect transcript name was provided i.e.,
    The transcript does not exist in the FASTA file of the
    transcriptome or the transcript name in the SAM alignment is
    different.

    You can check the history to make sure that the transcript names in the
    SAM file and the FASTA file are in the same format.

    Solution:
    Input transcript name as in the FASTA file of the transcriptome.
    If the FASTA header of the transcript starts with

    >CUFF.10354.1
    TCGCTGCACACCTGGTTATATAGCGTTTGGATTGTG...


    enter CUFF.10354.1 under "Name of the transcript to be plotted" in the
    Plot Ribosome Profile tool.

    It is also important to note that the same transcriptome should be used for
    the original alignment of the FASTQ reads (RiboSeq/RNASeq). This way, the
    generated SAM file will contain transcript names in the same format as in
    the FASTA file of the transcriptome.
  2. There are no reads corresponding to the given footprint length within the
    coding region for the transcript.

    Solution:
    Please try again with different transcript(s).
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