Daniel:Notebook/GenomeMiner/2013-9-5

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Revision as of 19:24, 5 September 2013 by >Djacobse (Created page with "=HL155= Back to Calendar ==Probecounts on Unfiltered Reverse Compliment Reads== From Matt's previous reverse compliment analysis on Bowtie, ...")
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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