Daniel:Notebook/GenomeMiner/2013-10-8

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Revision as of 17:55, 8 October 2013 by >Djacobse (→‎V4S1)
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HL155 Novoalign (Started 10/3/2013)

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V4S1

Calmd

samtools calmd -eS novo_v4s1_sortfilt.sam V4S1_fullrevcomp.fa > novo_v4s1_sortfilteq.sam

Perl Script

perl count_mismatch.plx

Error Counting Results

Error Rate: 5.42%
Error Rate of Insertions: 2.22%
Error Rate of Deletions: 2.15%
Error Rate of Substitutions: 1.05%

V4S2

Build Index

novoindex index_v4s2fullrevcomp.ndx V4S2_fullrevcomp.fa

Novoalign

novoalign -d index_v4s2fullrevcomp.ndx -f ../../s_3_1_Indx12.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s2.sam