User: dcassol

gravatar for dcassol
dcassol100
Reputation:
100
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New User
Location:
Riverside/CA
Last seen:
5 months, 4 weeks ago
Joined:
1 year, 5 months ago
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d*********@gmail.com

Posts by dcassol

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Hi Simon, In the example code/demo data, the reads in each of the fastq files should have the same length. Since the reads in your files have a variable length from 35-100bp (not sure if the reads have been gone through some tail trimming already), I believe that is the issue. Could you please try ...
written 10 months ago by dcassol100
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Hi @gocougs, Could you please share (e.g. via Dropbox or Google Drive) an example with just one set of your paired end fastq files where each contains the first 100,000 reads in order to try reproduce the error?​ Thank you very much for all the feedback.  Daniela ...
written 10 months ago by dcassol100
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... preprocessReads() uses internally the FastqStreamer function from the ShortRead package to stream through large FASTQ files in a memory-efficient manner. The argument batchsize is the number of reads to process in each iteration by the FastqStreamer function. How many reads do your files have?  I su ...
written 10 months ago by dcassol100
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... It does not seem to be something with the package and/or the code since it works with the demo data. The raw fastq data are being aligned with Tophat2 probably because somehow the software can handle/ignore some issue in the sequences, which does not occur in the preprocessReads() function. Could yo ...
written 10 months ago by dcassol100
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Hi @gocougs, Could you please provide the output of sessionInfo() executed in an R session right after the error occurred? In addition, did you try the same command line with the demo data? If not, could you please try to see if the same error occurs. ...
written 10 months ago by dcassol100

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