Daniel:Notebook/GenomeMiner/2013-9-5

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HL155

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Probecounts on Unfiltered Reverse Compliment Reads

From Matt's previous reverse compliment analysis on Bowtie, I'm doing probecount statistics on the unfiltered reads. The counts done on Tuesday were on the filtered reads. Since Matt's statistics were done on unfiltered reads, I'm doing this analysis to be consistent. Matt said that the filtering was done to prevent error counting on bad reads. However, those reads were still likely the probe they said they were, but the bases were not high quality. As such, the unfiltered reads will give more accurate counts.

Print 3rd Column (Name Column)

awk '{print $3}' V4S1/V4S1_bowtie2.sam > /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/unfilt_revcomp_Matt/v4s1_list.txt

Grep successful reads only

grep Probe v4s1_list.txt > v4s1_greplist.txt

Substitute Matt's probe names for mine (for perl script)

:%s/Probe/Probe_set1_/g

Perl Script File:Probecount by set.txt

perl probecount_by_set.plx > v4s1_rc_unfilt.csv

Copy to my computer for MATLAB analysis

scp djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/unfilt_revcomp_Matt/v4s1_rc_unfilt.csv ./