SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
I have a problem installin miRDeep2 Black_data_ho Bioinformatics 1 02-04-2016 02:14 AM
mirdeep2 "is not an id of the genome" problem florek Bioinformatics 1 08-26-2014 06:04 PM
Some problem with the perl wrapper in mirdeep2 potterbond007 Bioinformatics 2 07-14-2014 11:34 PM
miRDeep2 problem unique379 Bioinformatics 3 03-05-2014 07:24 PM
problem to launch miRDeep2 by PBS unique379 Bioinformatics 3 12-05-2013 03:23 AM

Reply
 
Thread Tools
Old 07-12-2016, 05:31 AM   #1
newfie
Junior Member
 
Location: Corner Brook

Join Date: Feb 2016
Posts: 8
Default Problem with mirdeep2

I have a problem with mapper.pl when i input my fasta file containing the reads.

here is the command and the error that i get:

mapper.pl N1_S1.fa -c -p ~/Desktop/bowtiebuild/cod_index -m -s /home/Desktop/cod/collapsed_reads/N1_S1_collapsed.fa -t ~/Desktop/cod/arf_files/N1_S1.arf

First line of FASTA reads file is not in accordance with the fasta format specifications
Please make sure your file is in accordance with the fasta format specifications and does not contain whitespace in IDs or sequences


***** Please check if the option you used (options c) designates the correct format of the supplied reads file N1_S1.fa *****

Here are the first few lines of my FASTA file:

>@NS500451:29:H3T2FBGXX:1:11101:15273:1059 1:N:0:ATCACG
GNGCTACTGGTGAAAT
>@NS500451:29:H3T2FBGXX:1:11101:21477:1064 1:N:0:ATCACG
ANTGGATAGCGCATTGGTA
>@NS500451:29:H3T2FBGXX:1:11101:23355:1065 1:N:0:ATCACG
GNTGTCGTGGCCGAGTGGTTAAGGAAATA

The command that i sued to convert fastq to fasta file is

awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' ~/Desktop/N1_S1_trimmed.fastq > ~/Desktop/N1_S1.fa

Important note: I had this problem when i was using mirdeep2 mapper.pl script in the linux server. But in my own linux machine the mapper.pl generated the collapsed reads and the arf files without any error code. So if there are whitespaces in the identifiers, how come the script doesn't generate any errors when i run in my own linux machine but not in the server?

Do anyone know how to fix this problem?
newfie 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 09:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO