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]]
|}


'''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]

Back to Calendar

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.png

Company Comparison

File:Hl155 compare rc.png