Editing
Daniel:Notebook/GenomeMiner/2013-9-12
(section)
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!
==Bowtie on Perfect Mock Sequence Data with Perfect Base Qualities== Based on the results from [[Daniel:Notebook/GenomeMiner/2013-9-11|yesterday]] I'm seeing what kind of alignment bowtie2 does on perfect sequences with perfect base qualities. Yesterday's sequences were direct copies of the .fa file, but they used base qualities randomly picked from the original sequencing data. These base qualities are all I (an extremely high quality score for phred33). Generated using MATLAB (''MockHL155_Master, Switch 3'') '''scp to Genome Miner''' scp V4S1_mockseq_perfseqbqual.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/ '''bowtie2''' bowtie2 -x bbuild_v4s1 -U v4s1_mockseq_perfseqbqual.fq --phred33 -S mockseq_v4s1_perfseqbqual.sam '''Alignment Results''' 2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 2953000 (99.80%) aligned exactly 1 time 6000 (0.20%) aligned >1 times 100.00% overall alignment rate So it looks like even with indisputable base quality and sequences, about 0.2% of sequences are so close that bowtie2 thinks they can be several sequences. '''Convert Sam to Bam and Sort''' samtools view -bS mockseq_v4s1_perfseqbqual.sam | samtools sort - mockseq_v4s1_perfseqbqual_sort '''Filter and Convert Back to Sam''' samtools view -h -F 4 -q 8 mockseq_v4s1_perfseqbqual_sort.bam > mockseq_v4s1_perfseqbqual_sortfilt.sam '''Replace Matched Pairs with Equals''' samtools calmd -eS mockseq_v4s1_perfseqbqual_sortfilt.sam V4S1.fa > mockseqv4s1perfseqbqual_sortfilteq.sam '''Perl Script Results''' script: [[File:imp_count_mismatch.txt]] Error Rate: 0 Error Rate of Insertions: 0 Error Rate of Deletions: 0 Error Rate of Substitutions: 0 Count: 2955000 perfect, 0 errors
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