Daniel:Notebook/GenomeMiner/2013-10-9: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
>Djacobse
Line 12: Line 12:
'''Novoalign'''
'''Novoalign'''
  novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam
  novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam
===Alignment Results===
#    Read Sequences: 11450664
#            Aligned:  4180484
#  Unique Alignment:  4172662
#  Gapped Alignment:  2905583
#    Quality Filter:    25772
# Homopolymer Filter:      38
#      Elapsed Time: 10011.583 (sec.)
#          CPU Time: 128.9 (min.)
# Done at Wed Oct  9 13:18:23 2013

Revision as of 23:35, 9 October 2013

HL155 Novoalign (Started 10/3/2013)

Back to Calendar

V4S3

Pipeline

Build Index

novoindex index_v4s3fullrevcomp.ndx V4S3_fullrevcomp.fa

Novoalign

novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam


Alignment Results

#     Read Sequences: 11450664
#            Aligned:  4180484
#   Unique Alignment:  4172662
#   Gapped Alignment:  2905583
#     Quality Filter:    25772
# Homopolymer Filter:       38
#       Elapsed Time: 10011.583 (sec.)
#           CPU Time: 128.9 (min.)
# Done at Wed Oct  9 13:18:23 2013