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

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
(Created page with "=HL155 Novoalign (Started 10/3/2013)= Back to Calendar ==V4S1 Novoalign (Changing Index Length)== ...")
 
>Djacobse
 
(4 intermediate revisions by the same user not shown)
Line 5: Line 5:
==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 16: Line 24:
  #          CPU Time: 154.0 (min.)
  #          CPU Time: 154.0 (min.)
  # Done at Tue Oct 15 16:24:52 2013
  # Done at Tue Oct 15 16:24:52 2013
===Error Counting Results===
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.

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.