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I am using sickle package from bioconda to trim my reads from the Illumina Miseq.

When I tried following code, it failed to run

sickle pe -t illumina -f file1   -r file2  -o output1  -p output2  -s combined_output -q 27 -l 25  

When I replaced illumina with sanger, it works. But my reads are from the illumina. Could anyone clarify if using this option is acceptable ? Also, what is the optimum value of -q and -l


Sickle examines quality and length quality thresholds via a sliding window. This assesses whether to trim the 3'-end of reads, for example removing a sudden drop in quality. It can also assess whether the quality of the 5' end is sufficiently high for trimming.

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It'd be rare to run into Illumina encoded quality scores any more, I doubt there are machines running that still produce those. Everything produced at the moment uses Sanger encoded (phred + 33) scores.

There is no optimum value for -q and -l, though reasonable values would typically be <=5 for -q and ~5 for -l.

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