miRNA analysis on EST sequences using miARMASeq

[ruchi]

Hi!!! I have 68506 EST sequences having length 500 to 1500bp. I have started from alignment step. where I’m getting error

"Reads file contained a pattern with more than 1024 sequence characters. Please truncate reads and quality values and and re-run Bowtie. Offending read: gi|71046429|gb|DR753987.1|DR753987"

Kindly suggest. Regards, Ruchi

[Eduardo Andres Leon]

Dear Ruchi, Are you using a fastq file from a NGS sequencer ?

Edu

[ruchi]

Dear Edu, I have downloaded ESTs from NCBI, that is in fasta format, then I have converted the same in fastq and given input in miARMa.

Ruchi

[Eduardo Andres Leon]

Hi again, Which aligner did you select? For a miRNA analysis, you can use bowtie1 (which has a read length limit of 1000bp) and bowtie2 (with no limit). If you select bowtie1, you have to consider bowtie2

Edu

[ruchi]

Hi again, Thanks for replying, now I have done with alignment. again the next problem I'm facing with readcount. I am getting the following error every time:

###################################################################

miARma, miRNA and RNASeq Multiprocess Analysis

miARma v 1.6.1 (Feb-2017)

Created at Computational Biology and Bioinformatics Group (CbBio)

Institute of Biomedicine of Seville. IBIS (Spain)

Copyright (c) 2017 IBIS. All rights reserved.

mail : [e-mail]

[Tue May 30 12:29:12 2017] Starting a miARma analysis for miRNA [Tue May 30 12:29:12 2017] Checking provided parameters for: ReadCount. [Tue May 30 12:29:12 2017] Checking General-output_dir parameter ... Exists! [Tue May 30 12:29:12 2017] The folder specified in (output_dir=Examples/basic_examples/miRNA/Known_miRNAs/results/) already exists. [Tue May 30 12:29:12 2017] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0 [Tue May 30 12:29:18 2017] Continue. [Tue May 30 12:29:18 2017] Checking ReadCount-database parameter ... error! ERROR Please check that the parameter database inside section [ReadCount] is correct.

I have attached the code and the database file too. Please suggest. Regards, Ruchi

[Eduardo Andres Leon]

Hi, Did you check that the GTF file is stored where you are pointing? :

Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf

We provide this file in the miRNA example: https://sourceforge.net/projects/miarma/files/Examples/Examples_miARma_miRNAs.tar.bz2

Edu

[ruchi]

yes, it is on the correct path.

[Eduardo Andres Leon]

ummm can you write the whole path to the file in the ini file ?

[ruchi]

Hi Eduardo' It worked. Thanks for helping me out.

Ruchi

[Eduardo Andres Leon]

Thanks to you for using miARma-Seq