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]

Back to Calendar

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.