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)
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