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.