915
edits
Changes
added instructions for barcode splitting
===Filter Sequences Using FastX-Toolkit===
# If samples are barcoded use Fastx barcode splitter (see http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_barcode_splitter_usage for more details):
<pre>
/usr/local/bin/fastx_barcode_splitter.pl --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol|--eol] [--mismatches N] [--exact] [--partial N] [--help] [--quiet] [--debug]
</pre>
* This requires a barcode file in the format where BC# is the barcode number and the nucleotide names are the barcodes:
<pre>
#This line is a comment (starts with a 'number' sign)
BC1 GATCT
BC2 ATCGT
BC3 GTGAT
BC4 TGTCT
</pre>
* This file is the FILE for the --bcfile option
* Example command where s_2_100.txt is the original file, mybarcodes.txt is the barcode file, 2 mismatches are allowed (default is 1). This will generate files /tmp/bla_BC#.txt:
<pre>
cat s_2_100.txt | /usr/local/bin/fastx_barcode_splitter.pl --bcfile mybarcodes.txt --bol --mismatches 2 \
--prefix /tmp/bla_ --suffix ".txt"
</pre>
# Filter for quality, if applicable
# Trim, if applicable