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NOTES.md

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Notes

GSE196816-GPL31944

  • Sample Number manually changed from 15 to 14 because dupRadar exceeded the 4h running time limit for some samples.
    • Sample SRR18042665 was manually removed because dupRadar exceeded the 4h running time limit.

GSE196192-GPL11154

  • Sample Number manually changed from 31 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE181143-GPL20795

  • Sample Number manually changed from 560 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE156422-GPL24676

  • Sample Number manually changed from 78 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE165709-GPL20301

  • Sample Number manually changed from 100 to 0 because GSE165709-GPL20301 is a duplicate of GSE165708-GPL20301.

GSE182239-GPL11154

  • Sample Number manually changed from 27 to 0 because fasterq-dump did not produce expected fastq files.

GSE158769-GPL11154

  • Sample Number manually changed from 1 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE160184-GPL18573

  • Sample Number manually changed from 12 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE161829-GPL24676

  • Sample Number manually changed from 106 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE148036-GPL21290

  • Sample Number manually changed from 20 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE114192-GPL18573

  • Shell script was updated to newer syntax with fasterq-dump run as a subshell command in the /scratch/$USER directory.

GSE139327-GPL18573

  • Sample Number manually changed from 28 to 26 because STAR found samples with very poor alignment rates.
    • Sample SRR10341042 was manually removed because STAR had a very poor alignment rate.
    • Sample SRR10341044 was manually removed because STAR had a very poor alignment rate.

GSE148829-GPL24676

  • Sample Number manually changed from 1 to 0 because GEO sample identifiers could not be translated to SRA identifiers.

GSE145648-GPL24676

  • Sample Number manually changed from 21 to 0 because fasterq-dump did not produce expected fastq files.

GSE145647-GPL24676

  • Sample Number manually changed from 21 to 0 because fasterq-dump did not produce expected fastq files.

GSE122619-GPL17303

  • Shell script was updated to newer syntax with fasterq-dump run as a subshell command in the /scratch/$USER directory.

GSE132300-GPL18573

  • Sample Number manually changed from 1 to 0 because fasterq-dump did not produce expected fastq files.

GSE122083-GPL18573

  • Sample Number manually changed from 2 to 0 because fasterq-dump did not produce expected fastq files.

GSE103147-GPL11154

  • Sample Number manually changed from 1650 to 1649 because fasterq-dump did not produce expected fastq files.
    • Sample SRR5981844 was manually removed because fasterq-dump did not produce *{1,2}.fastq files.

GSE70478-GPL15159

  • Sample Number manually changed from 32 to 0 because Experiment Type was Non-coding RNA profiling by array.