Editing
Matt:LabNotes/2014-11-1
(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!
====Create Target File v2: Target consitutive exons (no crossing exon boundaries)==== *Changed the algorithm to only select intervals that don't contain boundaries of exons (like constitutive exons but doesn't have to be present in all transcripts) **Ordered all boundaries from least to great regardless if start or stop ***In another array of equal size kept track of whether it was start or stop boundary **Selected intervals that on the left have a start boundary and on the right has a stop boundary with no boundaries in the middle *[[Media:CreateTargetFile_v2.txt | CreateTargetFile_v2.pl]] **input: biomart_export_newGenes.txt **output: target_file_newGenes.txt *Tested with one gene and two genes consisting of multiple overlapping exons **Runs with warnings but behaves correctly **Hash for converting Ensembl to HUGO missed a few genes due to multiple Ensembl Gene IDs for same HUGO IDs so had to do them manually ***KCNMB2 ***NBPF15 ***NEFL *[[Media:SortTargetFilesByChr.txt | sortTargetFilesByChr.pl]] **Removes 25bp from each end of target **Switch strand from + to - and - to + **Also runs with warnings that 'given' and 'when' are experimental
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