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

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

Revision as of 17:23, 8 October 2013

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

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