Daniel:Notebook/GenomeMiner/2013-9-24

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Mock HL155 (Started 9/9/2013)[edit]

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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%