Difference between revisions of "5. Trimming"
(Created page with "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/sha...") |
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$ java -jar /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar -h | $ java -jar /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar -h | ||
Usage: | Usage: | ||
| − | PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U><outputFile2P> <outputFile2U>] <trimmer1>... | + | PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] |
| + | [-baseout <outputBase> | <outputFile1P> <outputFile1U><outputFile2P> <outputFile2U>] <trimmer1>... | ||
or: | or: | ||
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:
