SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Working in MiReap njsphd Bioinformatics 1 01-03-2014 10:13 AM
MIREAP - optimizing options for different species? tjcarr Bioinformatics 0 09-16-2013 11:41 AM
Tophat Error: Error: segment-based junction search failed with err =-6 sjnewhouse RNA Sequencing 8 03-19-2013 05:14 AM
Tophat 2 error: Parse error at line 297359: missing colon in auxiliary data magbju RNA Sequencing 2 01-15-2013 04:57 AM
tophat2 segment_juncs error: Error: segment-based junction search failed with err =-6 [email protected] Bioinformatics 1 04-16-2012 07:37 AM

Reply
 
Thread Tools
Old 04-14-2015, 11:42 AM   #1
vilperte
Junior Member
 
Location: Brazil

Join Date: Aug 2014
Posts: 5
Default Error in MIREAP

Hello.

I'm trying to run MIREAP to predict novel miRNAs in my dataset.
However, when I run the script, the following message appears:

Can't use an undefined value as an ARRAY reference at ./bin/mireap.pl line 714.

When I run the test file, the message does not appear and the result are correct. So I'm guessing the problem is my input data and not the script itself.

One of my guessing is the read fasta file, which, according to the READ ME file, has to contain collapsed reads with modified read_ID (>t0000001 15, >t0000002 45, and so on). My file does not follow exactly this example (mine is >rr1 15, >rr2 45, and so on) because I did not find a script to do that. Does any one know a script for doing the exactly same read_ID?

Or does any one know what the problem might be, if not this one?

I would appreciate any feedback.

Kind regards,

Vinicius
vilperte is offline   Reply With Quote
Old 07-04-2017, 01:29 AM   #2
abhi4.amity
Junior Member
 
Location: lucknow

Join Date: Oct 2013
Posts: 1
Default

I have problem with mireap's mapping file. In mireap, i do not understand -m (map.txt) option. mireap is using for novel mirna prediction. I am not able to understand which software generate this file(map.txt). I do not understand the format of file.Can you please explain.
abhi4.amity is offline   Reply With Quote
Old 09-18-2018, 03:23 AM   #3
Operation_DeepSea
Junior Member
 
Location: India

Join Date: Jan 2018
Posts: 1
Default

I know the question is very old, but still want to reply for future users.

You need to generate the map.txt file by mapping ur microRNA reads to ur genome or transcriptome using bowtie or some other tool.

I did mapping using mapper.pl script from mirdeep2 software module.
Operation_DeepSea is offline   Reply With Quote
Reply

Tags
mireap, mirna, prediction

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 08:38 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO