Thread: Reliability
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Old 11-20-2009, 06:01 AM   #1
Location: London

Join Date: Sep 2008
Posts: 58
Default Reliability

I am comparing the output from Bowtie and maq and using the command below I get a total of 147-e6 alignments for 34-e6 reads. After rigorous filtering, I have half the numbers of reads mapped to chr1 as I did using maq. One of the issues is this:
HWI-EAS261:6:61:525:1199#0/2 - gi|89161185|ref|NC_000001.9|NC_000001 78 TAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAAC
HWI-EAS261:6:61:525:1199#0/2 + gi|89161205|ref|NC_000003.10|NC_000003 199384671 GTTAGGGTTAGGGTTGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA

Maq flags the second alignment with an MAQ score<10 and is thus easy to eliminate maintaining the 1st alignment.
Is it possible to know which alignment is correct from Bowtie?

./bowtie -t h_sapiens_asm -1 sanger1.fq -2 sanger2.fq -n 2 -l 28 -e 70 -I 0 -X 250 -a > output.txt --un unmapped_reads.fq --al reads_at_least_1_alignment.txt
#Reported 73,823,285 paired-end alignments to 1 output stream(s)

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