Daniel:Notebook/GenomeMiner/2013-9-5: Difference between revisions
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'''Comparing Filtered/Unfiltered reads''' | '''Comparing Filtered/Unfiltered reads''' | ||
[[Image: | Unfiltered counts on the right, filtered counts on the left | ||
{|class="wikitable" | |||
[[Image:Hl155_unfilt_probecount_mycro_bar.png|400px]]|[[Image:Hl155_filterrevcomp_mycro_bar.png|400px]] | |||
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'''Company Comparison''' | '''Company Comparison''' | ||
[[Image:Hl155_compare_rc.png|600px]] | [[Image:Hl155_compare_rc.png|600px]] |
Latest revision as of 23:10, 5 September 2013
HL155[edit]
Probecounts on Unfiltered Reverse Compliment Reads[edit]
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[edit]
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[edit]
Comparing Filtered/Unfiltered reads
Unfiltered counts on the right, filtered counts on the left
File:Hl155 unfilt probecount mycro bar.png|File:Hl155 filterrevcomp mycro bar.pngCompany Comparison