Daniel:Notebook/GenomeMiner/2013-10-8

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HL155 Novoalign (Started 10/3/2013)[edit]

Back to Calendar

V4S1[edit]

Calmd

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

Perl Script

perl count_mismatch.plx

Error Counting Results[edit]

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

V4S2[edit]

Pipeline[edit]

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

Convert to Bam and Sort

samtools view -bS novo_v4s2.sam | samtools sort - novo_v4s2_sort

Filter

samtools view -h -F 4 -q 70 novo_v4s2_sort.bam > novo_v4s2_sortfilt.sam

Calmd

samtools calmd -eS novo_v4s2_sortfilt.sam V4S2_fullrevcomp.fa > novo_v4s2_sortfilteq.sam

Perl Error Counting Script

perl count_mismatch.plx

Alignment Results[edit]

#     Read Sequences: 17308686
#            Aligned:  3672898
#   Unique Alignment:  3663803
#   Gapped Alignment:  2517060
#     Quality Filter:    44201
# Homopolymer Filter:       11
#       Elapsed Time: 14209.542 (sec.)
#           CPU Time: 179.1 (min.)
# Done at Tue Oct  8 14:17:27 2013

Error Counting Results[edit]

Error Rate: 5.47%
Error Rate of Insertions: 2.40%
Error Rate of Deletions: 1.96%
Error Rate of Substitutions: 1.11%