Daniel:Notebook/GenomeMiner/2013-7-31
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HL155[edit]
Started with the sam file of only mapped reads. Then printed the third column into text file.
Awk third column from SAM
awk '{print $3}' hrcp_onlymapped.sam > test.txt
Next I used perl to count the reads using this script:
#!usr/bin/perl #reads column 3 entries from hrcp_onlymapped_hl155.sam #finds probe entries "Probe_setn_m" and adds to probe counts of variable $probearray my @probearray = ([0]x19518,[0]x20000,[0]x18850,[0]x19301); my $set = 0; open READS, "test.txt"; while (<READS>) { if (/Probe/) { $set = 1 if (/set1/); $set = 2 if (/set2/); $set = 3 if (/set3/); $set = 4 if (/set4/); my ($probe,$junk,$num)=split /_/, $_; chomp($num); ++$probearray[$set][$num]; } } for (1..19517) { print "$probearray[1][$_],"; } print "$probearray[1][19518]\n"; for (1..19999) { print "$probearray[2][$_],"; } print "$probearray[2][20000]\n"; for (1..18849) { print "$probearray[3][$_],"; } print "$probearray[3][18850]\n"; for (1..19300) { print "$probearray[4][$_],"; } print "$probearray[4][19301]\n";
Copied probecount file back to my computer for processing in MATLAB.
SCP to laptop
%% scp <remote user>@<remote machine>:<remote path> <local file> scp djacobse@132.239.135.41:/home/djacobse/HL155/130628_HL155/probecount.csv probecount.csv