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Old 07-05-2014, 05:25 PM   #1
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Location: Baton Rouge, LA

Join Date: Jul 2014
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Default Problem calling Fastqc in Trim Galore?

When running Trim Galore, my .trimmed.fq file is blank and I get an error message. I suspect it is because Fastqc is not installed correctly (?). The output is pasted below. Thank you for any advice!

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Writing report to 'file2.fastq_trimming_report.txt'

Input filename: file2.fastq
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC'
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp

Writing final adapter and quality trimmed output to file2_trimmed.fq

>>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file file2.fastq <<<
sh: /~Programs/cutadapt: is a directory

0 sequences processed in total
Illegal division by zero at line 565.
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Old 07-05-2014, 11:26 PM   #2
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Location: Cambridge, UK

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It appears that you have specified the path to Cutadapt as the directory and not the executable. Appending cutadapt to the end of the path should fix that problem.

Cheers, Felix
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Old 07-06-2014, 05:17 AM   #3
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Location: Baton Rouge, LA

Join Date: Jul 2014
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Oh my goodness, silly mistake. Changing the path did fix the problem. Thank you very much Felix!
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