Editing
Dinh 2011/NOTES/2011-12-22
(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!
=Yi Zhang Lab (UNC) 24 ChIP/DIP Data= ==Analysis of enrichment in repeats== ===PE Data=== * FastqC on 100,000 reads READ1 (Indx15) [[File:YiZhang_24ChIP_PE_read1.png | 400px]] READ2 (Indx2) [[File:YiZhang_24ChIP_PE_read2.png | 400px]] * Trimming 5 bp from 5' of Read1 and 20 bp from 5' of Read2 * Sequence size is 300-600 (Alan's gel cut labnote) * Mapping procedure from BWA's manual: bwa aln ref.fa -b1 reads.bam > 1.sai bwa aln ref.fa -b2 reads.bam > 2.sai bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam * I expect that if the paired read flank onto repeats, one read will map uniquely while another will be mapped non-uniquely. BWA sampe will find the best unique mapping for the pair. * Trimming with BWA is most based on quality score, according to the manual, -q is : Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] Here is a nice diagram explaining this from SeqAnswers: [[File:bwaTrimming.jpg | 100px]] basically, trim where the average read quality from 3' end gets below the -q cutoff. Thus I will use -q 20 for trimming. * I will map all the fastq first using: bwa aln -l 28 -k 3 -t 16 -q 20 -I /media/disk-1/Dinh_Scratch/mm9Annotations-iGenomeUCSC/BWAIndex/mm9 ** checked that quality values are in ASCII-64! * Ran mapping.. 15.7% of bases are trimmed for Read 1
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