My analysis of miRNA doesn't work

[Former user]

Hello, i'm new on miARma and bioinformatics analysis in general so maybe I can fully expressed my problem properly.

I'm trying to analyse a paired miRNA GEOdataset series on the program, but still gives me separed results (not paired/ with columns of the seq 2).

miARma, miRNA and RNASeq Multiprocess Analysis #

miARma v 1.7.5 (May-2018)

Created at Computational Biology and Bioinformatics Group (CbBio)

Institute of Biomedicine of Seville. IBIS (Spain)

Modified and Updated at Bioinformatics Unit at IPBLN-CSIC

Institue for Parasitology and Biomedicine Lopez-Neyra (IPBLN-CSIC).

Granada (Spain)

Copyright (c) 2018 IBIS & IPBLN. All rights reserved.

mail : [e-mail]

[Wed Jun 22 14:19:56 2022] Starting a miARma analysis for miRNA [Wed Jun 22 14:19:56 2022] Checking provided parameters for: Quality,Aligner,ReadCount. [Wed Jun 22 14:19:56 2022] Checking General-output_dir parameter ... Exists! [Wed Jun 22 14:19:56 2022] The folder specified in (output_dir=/home/usertemp/NGS/miARma/results/results_a1/) already exists. [Wed Jun 22 14:19:56 2022] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0 [Wed Jun 22 14:20:02 2022] Continue. [Wed Jun 22 14:20:02 2022] All parameters are correct. [Wed Jun 22 14:20:02 2022] Starting Quality Analysis. [Wed Jun 22 14:20:36 2022] Quality Analysis finished. [Wed Jun 22 14:20:36 2022] No processed files are found [neither cutadapt, nor reaper nor adaptrimming folders], assuming /home/usertemp/NGS/miARma/reads/a1/ don't need to be proccessed [Wed Jun 22 14:20:36 2022] Starting a "Bowtie1" Alignment Analysis [Wed Jun 22 14:31:21 2022] "Bowtie1" Alignment Analysis finished [Wed Jun 22 14:31:21 2022] Starting a Readcount Analysis [Wed Jun 22 14:31:30 2022] Readcount Analysis finished. [Wed Jun 22 14:31:30 2022] miARma finished. Job took 11 minutes

the script used: [General] type=miRNA verbose=0 read_dir=/home/usertemp/NGS/miARma/reads/a1/ label=teste1 miARmaPath=. output_dir=/home/usertemp/NGS/miARma/results/results_a1/ organism=human threads=4 strand=yes stats_file=/home/usertemp/NGS/miARma/results/results_a1/miARma_stat.1090792.log logfile=/home/usertemp/NGS/miARma/results/results_a1/miARma_logfile.1090792.log setype= paired

[Quality] prefix=Pre

[Aligner] aligner=Bowtie1 bowtie1index=/home/usertemp/NGS/miARma/Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 bowtiemiss=0 bowtieleng=19 bowtie1parameters=--best --nomaqround

[ReadCount] database=/home/usertemp/NGS/miARma/Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf seqid=transcript_id quality=10 featuretype=miRNA ~

Also: I don't undestand that line:" No processed files are found [neither cutadapt, nor reaper nor adaptrimming folders], assuming /home/usertemp/NGS/miARma/reads/a1/ don't need to be proccessed " since in the file has the files of the geodata