Daniel:Notebook/GenomeMiner/2013-10-8: Difference between revisions

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>Djacobse
>Djacobse
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'''Convert to Bam and Sort'''
'''Convert to Bam and Sort'''
  samtools view -bS novo_v4s2.sam | samtools sort - novo_v4s2_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


===Alignment Results===
===Alignment Results===

Revision as of 23:43, 8 October 2013

HL155 Novoalign (Started 10/3/2013)

Back to Calendar

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

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

Alignment Results

#     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