Daniel:Notebook/GenomeMiner/2013-9-24: Difference between revisions

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I'll be running more of these tests today and tomorrow, but I'll talk more on that [[Daniel:Notebook/GenomeMiner/2013-9-25|tomorrow]].
I'll be running more of these tests today and tomorrow, but I'll talk more on that [[Daniel:Notebook/GenomeMiner/2013-9-25|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%

Revision as of 00:22, 25 September 2013

Mock HL155 (Started 9/9/2013)

Back to Calendar

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

Starting with this data, but there will be plenty more...

Workflow

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

Error Rate: 1.242%
Error Rate of Insertions: 0.192%
Error Rate of Deletions: 0.034%
Error Rate of Substitutions: 1.017%

Bash Script

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: File:Bwa-HL155bash.txt

Running More

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%