Editing
Daniel:Notebook/HiResChrPaint/2014-6-16
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!
=Probe Design= [[Daniel:Notebook/HiResChrPaint|Back to Calendar]] Using the Oligopaints scripts by Beliveau, my goal is to design a positive/negative control for the FISH probes. The control is to focus on a region of the X chromosome, yet to be determined. Using male cells (such as PGP1), exactly one region should be painted per cell. This serves as a potential positive and negative control. ==Probe Mining== '''Scripts:''' *[[Media:Oligopaints_Scripts_Manual.pdfβ|Oligopaints Scripts Manual]] *[[Media:Probe_mining_hox_example.pdf|Probe Mining Example]] Setting up the scripts for probe mining. I'm doing this locally on my machine for now, following the instructions in the two pdfs above. #Download fasta file from ncbi. ##[http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/|NCBI hg38 download] #Concatenate .fa files; oligopaints, etc. needs a single reference file ## cat *.fa > hg38.fa #Download gene information for a specific region ##Selected CASK gene, Xp11.4 (chrX:41514933-41923154); arbitrary #Generate BLAST database using makeblastdb ##make a directory called BlastDb ##set up a link using ln -s to the .fas file ##makeblastdb -in hg38.fas -out hg38 -dbtype nucl -parse_seqids #Run OligoArray to generate viable probe sequences ## java -jar /Users/danieljacobsen/Desktop/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d BlastDb/hg38 -o oligo_caskgene.txt -r rejected_oligo.fas -R caskgene.log -n 30 -l 60 -L 60 -D 1000 -t 55 -T 65 -s 70 -x 70 -p 35 -P 80 -m "CCCC;GGGG;TTTTT;AAAAA" -g 52 Error: Cannot run program "blastall": error=2, No such file or directory It would appear that the version of BLAST I downloaded is too new. The old version is known as blast legacy, and contains the command "blastall". The new version, blast+, uses the individual flags in blastall (blastn, blastp, etc) as their own standalone functions, and gets rid of "blastall". However, I examined genome miner, and it turns out genome miner is using the legacy version of blast, containing blastall. [[Daniel:Notebook/HiResChrPaint/2014-6-17|Tomorrow]], I'll have to try this again but one genome miner. [[Category:Probe Mining]] [[Category:HRCP]] [[Category:OligoArray]]
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