Daniel:Notebook/GenomeMiner/2013-9-5: Difference between revisions
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>Djacobse (Created page with "=HL155= Back to Calendar ==Probecounts on Unfiltered Reverse Compliment Reads== From Matt's previous reverse compliment analysis on Bowtie, ...") |
>Djacobse |
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'''Print 3rd Column (Name Column)''' | '''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 | 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:]] | |||
perl probecount_by_set.plx > v4s1_rc_unfilt.csv | |||
'''Copy to my computer for MATLAB analysis''' |
Revision as of 19:27, 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.
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:]]
perl probecount_by_set.plx > v4s1_rc_unfilt.csv
Copy to my computer for MATLAB analysis