Difference between revisions of "5. Trimming"
| Line 8: | Line 8: | ||
[-baseout <outputBase> | <outputFile1P> <outputFile1U><outputFile2P> <outputFile2U>] <trimmer1>... | [-baseout <outputBase> | <outputFile1P> <outputFile1U><outputFile2P> <outputFile2U>] <trimmer1>... | ||
or: | or: | ||
| + | SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>... | ||
Revision as of 15:55, 27 January 2016
We will use Trimmomatic for read trimming and filtering, and adapters removal.
Let’s see its general usage. To run trimmomatic you need to specify its full path: /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar):
$ java -jar /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar -h
Usage:
PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U><outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...
