Daniel:Notebook/GenomeMiner/2013-9-24
Jump to navigation
Jump to search
Mock HL155 (Started 9/9/2013)[edit]
Installed newest version of BWA (Burrows-Wheeler Aligner, 0.7.5a) today. Now I'm working on analyzing the data using the bwa aligner.
Mimic Error Data[edit]
Starting with this data, but there will be plenty more...
Workflow[edit]
1. bwa index -p fullrevcomp_v4s1 -a is V4S1_fullrevcomp.fa 2. bwa aln fullrevcomp_v4s1 V4S1_mockseq_error_mimic.fq > sacoord_v4s1mockseq_mimicerrror.sai 3. bwa samse fullrevcomp_v4s1 sacoord_v4s1mockseq_mimicerrror.sai V4S1_mockseq_error_mimic.fq > mockseqv4s1_errormimic_bwa.sam 4. samtools view -bS mockseqv4s1_errormimic_bwa.sam | samtools sort - mockseqv4s1_errormimic_bwa_sort 5. samtools view -h -F 4 -q 8 mockseqv4s1_errormimic_bwa_sort.bam > mockseqv4s1_errormimic_bwa_sortfilt.sam 6. samtools calmd -eS mockseqv4s1_errormimic_bwa_sortfilt.sam V4S1_fullrevcomp.fa > mockseqv4s1_errormimic_bwa_sortfilteq.sam
Error Counting Results[edit]
Error Rate: 1.242% Error Rate of Insertions: 0.192% Error Rate of Deletions: 0.034% Error Rate of Substitutions: 1.017%
Bash Script[edit]
The whole pipeline (1-6 + using Matt's perl counting script) has now been put in to a single bash file. Also necessary is Matt's perl script, but it doesn't need to be altered now. Bash script
Running More[edit]
I'll be running more of these tests today and tomorrow, but I'll talk more on that tomorrow.
Error Rate: 0.951% Error Rate of Insertions: 6.80e-06% Error Rate of Deletions: 2.04e-06 Error Rate of Substitutions: 0.951%