Disabling adapter removal

[Hoon Kim]

Hello,

I have miRNA sequencing where adapter sequencing has been already removed, and in this case, I think I had better to turn off "Adapter" in the miARma program. I wonder if you can let me know turn off the "Adapter" function. Probably, comment out 'adapter' in the "ini' file?

thank you in advance,

Hoon

[Hoon Kim]

Related to the above question, "Adapter" step in the miARma program caused an error with the sequencing data where adapter sequencing has been already removed, as follows:

#########################################################################
#   miARma, miRNA and RNASeq Multiprocess Analysis                      #
#                miARma v 1.5 (Apr-2016)                                #
#                                                                       #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Thu Jul 21 13:40:36 2016] Starting a miARma analysis for miRNA
[Thu Jul 21 13:40:36 2016] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction.
[Thu Jul 21 13:40:36 2016] Checking General-output_dir parameter ... Exists!
[Thu Jul 21 13:40:36 2016] The folder specified in (output_dir=/hkim6/work/merged-fastq/miARmaSeq/Known_miRNAs/results/) already exists.
[Thu Jul 21 13:40:36 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise:   0
[Thu Jul 21 13:40:42 2016] Continue.
[Thu Jul 21 13:40:42 2016] All parameters are correct.
[Thu Jul 21 13:40:42 2016] Starting Quality Analysis.
[Thu Jul 21 13:44:33 2016] Quality Analysis finished.
[Thu Jul 21 13:44:33 2016] Checking if files in folder: "/hkim6/work/merged-fastq/reads/" are in the correct fastq format.
[Thu Jul 21 13:44:33 2016] Starting a Adapter removal analysis
MINION ERROR :: system args failed: 256 (minion search-adapter -i /hkim6/work/merged-fastq/reads//S177_ATCGTT.fastq.gz -show 12  1>/tmp/minion.sq 2>> /hkim6/work/merged-fastq/miARmaSeq/Known_miRNAs/results/miARma_stat.3999.log)
Are you sure this fastq file contains and adapter sequence? at /hkim6/tools/miARmaSeq/cbbio-miarma-7440692e7bb9/lib/CbBio/RNASeq/Adapt.pm line 1538.

Your comments will be appreciated.

thank you in advance,

Hoon

[Hoon Kim]

I figured it out.

Thank you,