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

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>Djacobse
(Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar Installed newest version of BWA (Burrows-Wheeler Al...")
 
>Djacobse
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  1. bwa index -p fullrevcomp_v4s1 -a is V4S1_fullrevcomp.fa  
  1. bwa index -p fullrevcomp_v4s1 -a is V4S1_fullrevcomp.fa  
  2.
  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%

Revision as of 21:38, 24 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%