Daniel:Notebook/GenomeMiner/2013-9-5: Difference between revisions
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'''Copy to my computer for MATLAB analysis''' | '''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 ./ | scp djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/unfilt_revcomp_Matt/v4s1_rc_unfilt.csv ./ | ||
''HL155_Master.m; switches 9,10,11-unfiltered'' | |||
===Results=== | |||
'''Comparing Filtered/Unfiltered reads''' | |||
[[Image: | |||
'''Company Comparison''' | |||
[[Image:Hl155_compare_rc.png|600px]] |
Revision as of 22:10, 5 September 2013
HL155
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.
Workflow
Repeated for every set
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 ./
HL155_Master.m; switches 9,10,11-unfiltered
Results
Comparing Filtered/Unfiltered reads
[[Image:
Company Comparison