Daniel:Notebook/GenomeMiner/2013-10-2: Difference between revisions
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>Djacobse (Created page with "=HL155= Back to Calendar ==Novoalign Sequence Alignment== Running novoalign on the sequencing data from HL155 since novoalign seems to be th...") |
>Djacobse |
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==Novoalign Sequence Alignment== | ==Novoalign Sequence Alignment== | ||
Running novoalign on the sequencing data from HL155 since novoalign seems to be the best alignment software (detects errors most correctly). | Running novoalign on the sequencing data from HL155 since novoalign seems to be the best alignment software (detects errors most correctly). Working off [[Matt:LabNotes/2013-9-27|Matt's previous methods]]. | ||
'''Build Index''' | '''Build Index''' | ||
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'''Run Novoalign''' | '''Run Novoalign''' | ||
nohup novoalign -d index_v4s1fullrevcomp.ndx -f ../../s_2_1_Indx11.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s1_s21indx11.sam & | |||
Issue here is that novoalign only runs on 1 fq at a time (I think). I'm going to see if I can cat the fq files before running. |
Latest revision as of 16:49, 3 October 2013
HL155[edit]
Novoalign Sequence Alignment[edit]
Running novoalign on the sequencing data from HL155 since novoalign seems to be the best alignment software (detects errors most correctly). Working off Matt's previous methods.
Build Index
novoindex index_v4s1fullrevcomp.ndx V4S1_fullrevcomp.fa
Run Novoalign
nohup novoalign -d index_v4s1fullrevcomp.ndx -f ../../s_2_1_Indx11.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s1_s21indx11.sam &
Issue here is that novoalign only runs on 1 fq at a time (I think). I'm going to see if I can cat the fq files before running.