Daniel:Notebook/GenomeMiner/2013-10-15: Difference between revisions
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>Djacobse |
>Djacobse |
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(2 intermediate revisions by the same user not shown) | |||
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novoindex -k 98 index_V4S1_fullrevcomp.ndx V4S1_fullrevcomp.fa | 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 | 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 | the rest of the [[media:Bash_HL155novo.txt|bash script]] | ||
===Alignment Results=== | ===Alignment Results=== | ||
# Read Sequences: 11450664 | # Read Sequences: 11450664 | ||
# Aligned: 4194879 | # Aligned: 4194879 | ||
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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]
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.