SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
miRDeep2 asaleh Bioinformatics 5 09-29-2017 03:29 AM
mirdeep2 bharat_iyengar Bioinformatics 0 12-25-2012 01:41 AM
The meaning of miRDeep2 score? louis7781x Bioinformatics 0 11-28-2012 02:27 AM
A question related to miRDeep2.pl cobrass Bioinformatics 0 10-10-2012 07:56 AM
mirdeep2 check mirna folding RTK45 Bioinformatics 1 03-26-2012 06:29 AM

Reply
 
Thread Tools
Old 01-21-2013, 06:34 AM   #1
ccstaats
Member
 
Location: Porto Alegre

Join Date: Jan 2012
Posts: 12
Default Randfol in miRDeep2

Hello all,
I am trying to get miRDeep 2 to work with my data.
Everything goes fine with mapping, collapsing, etc.
When I try to run the mirDeep2.pl using the script
Code:
perl mirDeep2.pl collapsed.fa Genome.fa collapsed_vs_Genome.arf none none none
the initial process work fine. Until Randfold! The pipeline stops in "computing randfold p-values". One nucleus stay at 100% activity.
How long is this process? Here, 2 h and still counting.
Thank you for your help.
Charley
ccstaats is offline   Reply With Quote
Old 01-22-2013, 11:31 AM   #2
ccstaats
Member
 
Location: Porto Alegre

Join Date: Jan 2012
Posts: 12
Default

Dear all.
I Just realized that the process is quite long. The data analysis (4 Gb of fasta files) runned in 3 hours in a I5 processor with 8gb RAM.
Thank you all.
Charley
ccstaats is offline   Reply With Quote
Old 01-25-2013, 03:21 PM   #3
jay2008
Member
 
Location: Australia

Join Date: Sep 2010
Posts: 44
Default

RNAfold is most time-consuming task in predicting miRNAs from deep sequencing. All current predicting tools miRDeep, miRTRAP, MIReNA, miRDeep* and etc. use similar RNA secondary structure prediction algorithm. but it is not necessary to use big memory for preducting RNA secondary structure.
jay2008 is offline   Reply With Quote
Old 06-12-2013, 06:40 AM   #4
JonB
Member
 
Location: Norway

Join Date: Jan 2010
Posts: 83
Default

Hi,

I'm having trouble making randfold 2.0. I have the SQUID libraries but get this message when making randfold:

Code:
-bash-4.1$ make
gcc -O3 -I.  -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid 
randfold.c:24:18: error: squid.h: No such file or directory
randfold.c:26:23: error: sre_random.h: No such file or directory
randfold.c: In function 'main':
randfold.c:30: error: 'SQFILE' undeclared (first use in this function)
randfold.c:30: error: (Each undeclared identifier is reported only once
randfold.c:30: error: for each function it appears in.)
randfold.c:30: error: 'sqfp' undeclared (first use in this function)
randfold.c:38: error: 'SQINFO' undeclared (first use in this function)
randfold.c:38: error: expected ';' before 'sqinfo'
randfold.c:89: warning: incompatible implicit declaration of built-in function 'strcpy'
randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this function)
randfold.c:100: error: 'sqinfo' undeclared (first use in this function)
randfold.c:103: warning: incompatible implicit declaration of built-in function 'malloc'
randfold.c:103: warning: incompatible implicit declaration of built-in function 'strlen'
randfold.c:136: warning: incompatible implicit declaration of built-in function 'fabs'
randfold.c:158: warning: incompatible implicit declaration of built-in function 'free'
make: *** [randfold] Error 1
I am quite a novise when it comes to these things. Should I perhaps configure the makefile?
JonB is offline   Reply With Quote
Old 09-29-2017, 03:34 AM   #5
gurjeet
Junior Member
 
Location: india

Join Date: Sep 2017
Posts: 2
Question rndfold in mirdeep 2

I recently done small RNA sequencing of my endocrine tumour samples. I got result analysis with Mirdeep2 . I am not master in bioinformatics so , i outsourced the analysis. The company have predicted some novel micrornas. They have used mirdeep2 software for predicting novel microRNA.
I am facing problem in selecting novel microRNAs from small RNA sequencing. Is it necessary to have high mirdeep2 score with high mature read count. Those sequence with high mirdeep2 score ( like 3168) & mature read count (456) have non significant RANDFOLD p value. I am confused in this part.
Basically , I want to validate the results using PCR. But i am facing alot of problem in selecting top 5 novel microRNAs. I read in mirdeep2 documentation in which the score cut was from -10 to 10.
Please guide me regarding mirdeep2 software and please help me its parameters for selecting novel microRNA.I will be very thankful to you.
thanks.
Regards
gurjeet 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 04:00 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO