Stacks

process_shortreads

Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.

Program Options

process_shortreads [-f in_file | -p in_dir [-P] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir
[-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h]

Barcode options:

Adapter options:

Output options:

Advanced options:

Example Usage

If your data are paired-end, Illumina HiSeq data, in a directory called raw:

~/raw% ls lane4_NoIndex_L004_R1_001.fastq lane4_NoIndex_L004_R1_009.fastq lane4_NoIndex_L004_R2_005.fastq lane4_NoIndex_L004_R1_002.fastq lane4_NoIndex_L004_R1_010.fastq lane4_NoIndex_L004_R2_006.fastq lane4_NoIndex_L004_R1_003.fastq lane4_NoIndex_L004_R1_011.fastq lane4_NoIndex_L004_R2_007.fastq lane4_NoIndex_L004_R1_004.fastq lane4_NoIndex_L004_R1_012.fastq lane4_NoIndex_L004_R2_008.fastq lane4_NoIndex_L004_R1_005.fastq lane4_NoIndex_L004_R2_001.fastq lane4_NoIndex_L004_R2_009.fastq lane4_NoIndex_L004_R1_006.fastq lane4_NoIndex_L004_R2_002.fastq lane4_NoIndex_L004_R2_010.fastq lane4_NoIndex_L004_R1_007.fastq lane4_NoIndex_L004_R2_003.fastq lane4_NoIndex_L004_R2_011.fastq lane4_NoIndex_L004_R1_008.fastq lane4_NoIndex_L004_R2_004.fastq lane4_NoIndex_L004_R2_012.fastq

Then you run process_shortreads like this:

% process_shortreads -P -p ./raw/ -o ./samples/ -b ./barcodes/barcodes_lane4 -r -c -q

See more examples in the process_radtags manual page.

Other Pipeline Programs

Raw Reads

Core

Execution control

Utilities