Editing
Matt:LabNotes/2013-8-27
(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!
====Checking Error Rate for V4S1==== # Read Sequences: 11450664 # Aligned: 1061 # Unique Alignment: 1061 # Gapped Alignment: 1061 # Quality Filter: 23301 # Homopolymer Filter: 40 # Elapsed Time: 10198.104 (sec.) # CPU Time: 164.2 (min.) # Done at Fri Aug 30 14:34:36 2013 samtools view -bS V4S1_novoalign.sam | samtools sort - V4S1_novoalign_sorted samtools view -h -F 4 -q 70 V4S1_novoalign_sorted.bam > V4S1_novoalign_sorted_filtered.sam samtools calmd -eS V4S1_novoalign_sorted_filtered.sam Probelist_V4S1.fa > V4S1_novoalign_sf=.sam (After the first 30 bases, ALL WRONG (insertions)) perl Count_mismatches_from_novoalignSAMquantifyOligo.pl -> CountMismatches_calmd_V4S1_novoalign.txt Error Rate: 0.44586038961039 = 44.6%<br> Error Rate of Insertions: 0.0739448051948052 = 7.4%<br> Error Rate of Deletions: 0.368181818181818 = 36.8%<br> Error Rate of Substitutions: 0.00373376623376623 = 0.37%<br> *Realized Mistake in MYcroArray Reference Sequences: http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-8-30
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