Daniel:Notebook/GenomeMiner/2013-8-7: Difference between revisions

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(Created page with "=HL155= Back to Calendar Continuing the analysis of the HL155 data. I looked through the information on the bowtie2 manual.")
 
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]]
[[Daniel:Notebook/GenomeMiner|Back to Calendar]]


Continuing the analysis of the HL155 data.  I looked through the information on the bowtie2 manual.
Continuing the analysis of the HL155 data.  I looked through the information on the [http://computing.bio.cam.ac.uk/local/doc/bowtie2.html bowtie2 manual].  The 12th column of a SAM output contains several possibly useful pieces of information:
 
''From Bowtie2 manual''
'''XM:i:<N>''' The number of mismatches in the alignment. Only present if SAM record is for an aligned read.
'''NM:i:<N> The edit distance; that is, the minimal number of one-nucleotide edits (substitutions, insertions
and deletions) needed to transform the read string into the reference string. Only present if SAM record is for
  an aligned read.
 
Basically, these should be able to give me an idea of the number of mismatches.  I'm not really sure yet whether XM or NM is better, so I'm taking them both.  First I awked the data from the 3rd, and 12-20th columns.
 
'''Awk Command'''
awk '{print $3,\t,$12,\t,$13,\t,$14,\t,$15,\t,$16,\t,$17,\t,$18,\t,$19,\t,$20}' hcrp_onlymapped_hl155.sam >
/home/djacobse/hl155/hl155_3_12_andbeyond.txt
 
'''Perl Script'''
#!usr/bin/perl
use strict;
use warnings;
#should count the NM:i:digit column of the script and return
#the probe name, mismatches, and edit number
open READS, "hl155_3_12_andbeyond.txt";
while (<READS>) {
my($probe)=$_=~/(Probe_set\d_\d\d?\d?\d?\d?)/;
my($mismatch) = $_ =~/(XM:i:\d)/;
my($mismatch2)= $mismatch =~ /(\d)/ ;
my($editnum)= $_ =~ /(NM:i:\d)/;
my($editnum2) = $editnum =~ /(\d)/;
print $probe."\t".$mismatch2."\t".$editnum2."\n";
}
 
'''SCP to Laptop'''
scp djacobse@132.239.135.41:/home/djacobse/hl155/hl155_mismatch_error.txt hl155_mismatch_error.txt
 
Read in matlab, calculated the mean, standard deviation, median, and mode for both mismatch number and edit distance.
 
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="font-size:12pt" align="center"
| align="center" width="108" height="30" | &nbsp;
|style="font-weight:bold" width="65" | mean
|style="font-weight:bold" width="65" | standard deviation
|style="font-weight:bold" width="65" | median
|style="font-weight:bold" width="65" | mode
 
|- style="font-size:12pt" align="center"
|style="font-weight:bold" height="15" | mismatches (XM)
| align="center" | 0.5396
| align="center" | 0.7715
| align="center" | 0
| align="center" | 0
 
|- style="font-size:12pt" align="center"
|style="font-weight:bold" height="15" | edit distance (NM)
| align="center" | 1.5759
| align="center" | 1.3009
| align="center" | 1
| align="center" | 1
 
|}

Latest revision as of 18:39, 8 August 2013

HL155[edit]

Back to Calendar

Continuing the analysis of the HL155 data. I looked through the information on the bowtie2 manual. The 12th column of a SAM output contains several possibly useful pieces of information:

From Bowtie2 manual

XM:i:<N> The number of mismatches in the alignment. Only present if SAM record is for an aligned read.
NM:i:<N> The edit distance; that is, the minimal number of one-nucleotide edits (substitutions, insertions
and deletions) needed to transform the read string into the reference string. Only present if SAM record is for
 an aligned read.

Basically, these should be able to give me an idea of the number of mismatches. I'm not really sure yet whether XM or NM is better, so I'm taking them both. First I awked the data from the 3rd, and 12-20th columns.

Awk Command

awk '{print $3,\t,$12,\t,$13,\t,$14,\t,$15,\t,$16,\t,$17,\t,$18,\t,$19,\t,$20}' hcrp_onlymapped_hl155.sam >
/home/djacobse/hl155/hl155_3_12_andbeyond.txt

Perl Script

#!usr/bin/perl
use strict;
use warnings;
#should count the NM:i:digit column of the script and return
#the probe name, mismatches, and edit number
open READS, "hl155_3_12_andbeyond.txt";
while (<READS>) {
my($probe)=$_=~/(Probe_set\d_\d\d?\d?\d?\d?)/;
my($mismatch) = $_ =~/(XM:i:\d)/;
my($mismatch2)= $mismatch =~ /(\d)/ ;
my($editnum)= $_ =~ /(NM:i:\d)/;
my($editnum2) = $editnum =~ /(\d)/;
print $probe."\t".$mismatch2."\t".$editnum2."\n";
}

SCP to Laptop

scp djacobse@132.239.135.41:/home/djacobse/hl155/hl155_mismatch_error.txt hl155_mismatch_error.txt

Read in matlab, calculated the mean, standard deviation, median, and mode for both mismatch number and edit distance.

  mean standard deviation median mode
mismatches (XM) 0.5396 0.7715 0 0
edit distance (NM) 1.5759 1.3009 1 1