#6 Error in mirPRo while novel study

[Pravin Nilawe]

We are performing smal RNA analysis using 2 samples sequenced on Ion Proton system and utilized fastq format reads. We performed installations and checked them as instructed in README.

We started an analysis using 2 samples but it failed with an error saying "open error! ./result/SRR333597/SRR333597_novel_quantifier_report.csv".

I tried the same with the test data but it ended up with same error. Please provide me your comments and suggestions to resolve this issue at the earliest.

I am attaching within the log file generated on analysis.

Thanks & regards,
Pravin

[Jieming Shi]

Please check the novoalign version. It should be release V3.02.12.

[Pravin Nilawe]

The version is V3.02.12. still its giving the error.

On Thu, Apr 21, 2016 at 8:40 PM, Jieming Shi sjm888888@users.sf.net wrote:

Please check the novoalign version. It should be release V3.02.12.

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[tickets:#6] Error in mirPRo while novel study

Status: open
Milestone: 1.0
Labels: novel failed
Created: Thu Apr 21, 2016 12:36 PM UTC by Pravin Nilawe
Last Updated: Thu Apr 21, 2016 12:36 PM UTC
Owner: liangc_mu
Attachments:

nohup.out (2.0 MB; application/octet-stream)

We are performing smal RNA analysis using 2 samples sequenced on Ion Proton
system and utilized fastq format reads. We performed installations and
checked them as instructed in README.

We started an analysis using 2 samples but it failed with an error saying
"open error! ./result/SRR333597/SRR333597_novel_quantifier_report.csv".

I tried the same with the test data but it ended up with same error. Please
provide me your comments and suggestions to resolve this issue at the
earliest.

I am attaching within the log file generated on analysis.

Thanks & regards,
Pravin

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Pravin Nilawe
+919768129028

[Jieming Shi]

Can you tell me the command you used to run this program?

[Pravin Nilawe]

Version is V3.02.12. Still the problem exists.

[tiennes]

I had the same problem,
this resulted from forgetting to pass the option --other "insert related species here:mmu". Since mirpro generates the novelfind command with a mandatory "other option", I think it just dies because the option is not given.

cheers tiennes

[Jieming Shi]

You are right. "--other" is necessary for novel miRNA prediction.

[Pravin Nilawe]

Thanks everyone. I have just used this option and started an analysis. I would get back once the analysis is completed.
Thanks again.

Cheers
Pravin

[Pravin Nilawe]

Hello,

Thanks for your help and suggestions. I was able to run the software successfully.

But i found out that the mapping of reads onto the genome is very low and didnt produce any results. I have ion torren Proton system and have sequenced small RNA with a count of 30-40 million reads.

While going through the software novoalign, i found very less reads are aligning to the reference genoome and when searched across novoalign, they had a page information usage of certain parameters to get better alignment of reads.

Please can you suggest me, if i can some how utilize the commands provided in novoalign for ion torrent while executing mirpro. I think this should resolve my issues low number of reads mapping.

Please can you suggest and help resolve issue.

regards,
Pravin

[Jieming Shi]

Hello,

mirPRo supports some of the parameter settings of novoaligh (version V3.02.12). See follows:

--map-len <int>: minimum mapped length of reads which are mapped to precursor miRNAs; default = 15;
-o <int>: the gap opening penalty in novoalign mapping; default = 40;
-e <int>: the gap extend penalty in novoalign mapping; default = 6;
--map-score <int>: maximum mapping penalty score; default is 60;</int></int></int></int>

If you want a full parameter control of novoalign, you can use novoalign to map reads separately and then run program "bin/mirpro_samToArf" and "bin/mirpro_quantifier." in mirPRo package, to quantify the known miRNA in your samples.

To predict novel miRNAs, you can run "bin/mirpro_novelFinder" or miRDeep2 (https://www.mdc-berlin.de/8551903/en/) with the collapsed clean reads in FASTA format as input. Basiclly, two programs have same algorithm.

Help information can be obtained by command with no arguments, for example, 'bin/mipro_samToArf' (similar for other programs).

Good luck.