Daniel:Notebook/GenomeMiner/2013-10-17
HL155 Novoalign (Started 10/3/2013)[edit]
V4S1 Novoalign Threshold 75[edit]
From the Novoalign manual: "A threshold of 75 would allow for alignment of reads with two mismatches at high quality base positions plus one or two mismatches at low quality positions or to ambiguous characters in the reference sequence". This might be artificially reducing the read quality, but I think that setting a threshold might be the way to go. Also, this is just a test run so I used the -# 100K flag to only do the first 100,000 reads
Alignment Results[edit]
# Read Sequences: 100000 # Aligned: 15324 # Unique Alignment: 15311 # Gapped Alignment: 5697 # Quality Filter: 194 # Homopolymer Filter: 0 # Elapsed Time: 50.447 (sec.) # CPU Time: 0.4 (min.) # Done at Thu Oct 17 10:08:12 2013
Error Counting Results[edit]
Error Rate: 1.51% Error Rate of Insertions: 0.083% Error Rate of Deletions: 0.67% Error Rate of Substitutions: 0.75%
So this trial did have a lower error. However, comparing with Tuesday, the alignment rate here is ~15%, where as Tuesday was closer to 36%.
Bowtie2 Comparison[edit]
I want to make sure I am using similar values (threshold 75 was arbitrarily picked). Also, I want to check if bowtie and novoalign report the same MAPQ scores in SAM format.
Workflow[edit]
bowtie2-build -f V4S1_fullrevcomp.fa build_v4s1_bowtie bowtie2 -x build_v4s1_bowtie -U ../../s_2_1_Indx13.txt --phred64 -S bowtie_v4s1.sam -u 100000
Alignment Results[edit]
100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74433 (74.43%) aligned 0 times 25510 (25.51%) aligned exactly 1 time 57 (0.06%) aligned >1 times 25.57% overall alignment rate