fqtrim minimum read length default value
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This means any reads that gets shortened less than 16bp will be removed. Its clearly stated in manual.
minimum read length after trimming; if the read sequence is shorter than this, before or after the requested trimming filters, the read is discarded (trashed). Default: 16.
In other words, the shorted read will be 16bp after the trimming. All reads less than 16bp will be discarded.
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GouthamAtla
Default values will works for most of the datasets. They must have found it optimal value while testing the tool on a particular data set. BUT IT HIGHLY VARIABLE BETWEEN DATASETS. If they do not keep default values, you may need to enter tons of values while running the command.
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