SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing
Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie and ERANGE Bio.X2Y Bioinformatics 5 10-29-2010 06:41 AM
Erange MaloneJH RNA Sequencing 25 10-08-2010 06:11 AM
problem in using ERANGE saha RNA Sequencing 0 03-03-2010 10:31 PM
ERANGE problems! gthomas RNA Sequencing 1 01-12-2010 03:30 AM
ERANGE (makerdsfrombowtie.py) joseph Bioinformatics 0 05-13-2009 10:15 AM

Reply
 
Thread Tools
Old 04-08-2010, 10:02 PM   #1
sylee
Junior Member
 
Location: south korea

Join Date: Apr 2010
Posts: 3
Default ERANGE - getsplicefa.py

Hi, All..
I have a question related to "ERANGE" for RNA-seq analysis.

I got an empty file after running the "getsplicefa.py" script..

the following messege :

psyco not running
/B/sylee/ERANGE/commoncode/getsplicefa.py: version 3.2
60922
545588
10000enes
20000enes
30000enes
40000enes
50000enes
60000enes
3310 splices too short to be seen
634 splices will be under-reported


Any help is appreciable!
Thank you.
- sunyoung
sylee is offline   Reply With Quote
Old 06-29-2010, 09:31 AM   #2
David
Junior Member
 
Location: Baltimore Maryland

Join Date: Jul 2009
Posts: 5
Default

What was your exact command?
David is offline   Reply With Quote
Old 06-29-2010, 04:22 PM   #3
sylee
Junior Member
 
Location: south korea

Join Date: Apr 2010
Posts: 3
Default

I typed ..
$python getsplicefa.py human ~/genome_data/hg18/knownGene.txt hg18splice36.fa 32

Thank you!
sylee is offline   Reply With Quote
Old 06-30-2010, 04:25 AM   #4
David
Junior Member
 
Location: Baltimore Maryland

Join Date: Jul 2009
Posts: 5
Default

That looks correct. I would check your variables to make sure that they are pointing to the proper directories. PYTHONPATH and CISTEMATIC_ROOT should both be pointing to one directory above your Cistematic directory.
David is offline   Reply With Quote
Old 07-20-2010, 03:03 PM   #5
yh253
Member
 
Location: Ireland

Join Date: Jul 2009
Posts: 16
Default

Hi sylee,

Just wondering have you solved your problem?

I got the same problem as you that getsplicefa.py generated an empty file even I did check according to David's point.

Appreciate any commons.
yh253 is offline   Reply With Quote
Old 07-20-2010, 04:42 PM   #6
sylee
Junior Member
 
Location: south korea

Join Date: Apr 2010
Posts: 3
Default

sorry for late reply,..

yh253, I also haven't solved the problem yet..
David, PYTHON PATH and CISTEMATIC_ROOT were pointed to one directory above the Cistematic directory. but, I got empty file ...

regards,
sylee is offline   Reply With Quote
Old 07-22-2010, 07:50 AM   #7
yh253
Member
 
Location: Ireland

Join Date: Jul 2009
Posts: 16
Default

Sylee,

The problem is you should change the genome from 'human' to 'hsapiens' if you use Cistematic-3.0

Try:

$python getsplicefa.py hsapiens ~/genome_data/hg18/knownGene.txt hg18splice36.fa 32

Make sure: $PATHONPATH indicates where you keep all the ERANGE python script; and $CISTEMATIC_ROOT points to where you keep the 'H_sapiens' genome (downloaded from Cistematic website).
yh253 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off



All times are GMT -8. The time now is 09:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO