Editing
Daniel:Notebook/GenomeMiner/2013-10-17
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
=HL155 Novoalign ([[Daniel:Notebook/GenomeMiner/2013-10-3|Started 10/3/2013]])= [[Daniel:Notebook/GenomeMiner|Back to Calendar]] ==V4S1 Novoalign Threshold 75== From the Novoalign manual: "A threshold of 75 would allow for alignment of reads with two mismatches at high quality base positions plus one or two mismatches at low quality positions or to ambiguous characters in the reference sequence". This might be artificially reducing the read quality, but I think that setting a threshold might be the way to go. Also, this is just a test run so I used the -# 100K flag to only do the first 100,000 reads ===Alignment Results=== # Read Sequences: 100000 # Aligned: 15324 # Unique Alignment: 15311 # Gapped Alignment: 5697 # Quality Filter: 194 # Homopolymer Filter: 0 # Elapsed Time: 50.447 (sec.) # CPU Time: 0.4 (min.) # Done at Thu Oct 17 10:08:12 2013 ===Error Counting Results=== Error Rate: 1.51% Error Rate of Insertions: 0.083% Error Rate of Deletions: 0.67% Error Rate of Substitutions: 0.75% So this trial did have a lower error. However, comparing with [[Daniel:Notebook/GenomeMiner/2013-10-15|Tuesday]], the alignment rate here is ~15%, where as Tuesday was closer to 36%. ==Bowtie2 Comparison== I want to make sure I am using similar values (threshold 75 was arbitrarily picked). Also, I want to check if bowtie and novoalign report the same MAPQ scores in SAM format. ===Workflow=== bowtie2-build -f V4S1_fullrevcomp.fa build_v4s1_bowtie bowtie2 -x build_v4s1_bowtie -U ../../s_2_1_Indx13.txt --phred64 -S bowtie_v4s1.sam -u 100000 ===Alignment Results=== 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 74433 (74.43%) aligned 0 times 25510 (25.51%) aligned exactly 1 time 57 (0.06%) aligned >1 times 25.57% overall alignment rate
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information