Daniel:Notebook/GenomeMiner/2013-10-15: Difference between revisions

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==V4S1 Novoalign (Changing Index Length)==
==V4S1 Novoalign (Changing Index Length)==


Attempting to fix these issues with Novoalign by changing the k-mer length when creating the index.
===Pipeline===
novoindex -k 98 index_V4S1_fullrevcomp.ndx V4S1_fullrevcomp.fa
novoalign -d index_V4S1_fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM > v4s1_novo.sam
the rest of the [[media:Bash_HL155novo.txt|bash script]]


===Alignment Results===
===Alignment Results===
  #    Read Sequences: 11450664
  #    Read Sequences: 11450664
  #            Aligned:  4194879
  #            Aligned:  4194879
Line 23: Line 31:
  Error Rate of Deletions: 2.36%
  Error Rate of Deletions: 2.36%
  Error Rate of Substitutions: 4.09%
  Error Rate of Substitutions: 4.09%
So no, that really didn't do much.  I'll look into other options with novoalign to try and correct the error, or I'll do some post-processing.

Latest revision as of 17:19, 17 October 2013

HL155 Novoalign (Started 10/3/2013)[edit]

Back to Calendar

V4S1 Novoalign (Changing Index Length)[edit]

Attempting to fix these issues with Novoalign by changing the k-mer length when creating the index.

Pipeline[edit]

novoindex -k 98 index_V4S1_fullrevcomp.ndx V4S1_fullrevcomp.fa
novoalign -d index_V4S1_fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM > v4s1_novo.sam
the rest of the bash script

Alignment Results[edit]

#     Read Sequences: 11450664
#            Aligned:  4194879
#   Unique Alignment:  4178621
#   Gapped Alignment:  3042944
#     Quality Filter:    23301
# Homopolymer Filter:       40
#       Elapsed Time: 9373.277 (sec.)
#           CPU Time: 154.0 (min.)
# Done at Tue Oct 15 16:24:52 2013

Error Counting Results[edit]

Error Rate: 6.63%
Error Rate of Insertions: .179%
Error Rate of Deletions: 2.36%
Error Rate of Substitutions: 4.09%

So no, that really didn't do much. I'll look into other options with novoalign to try and correct the error, or I'll do some post-processing.