F Nadiya Nadiya

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Questions related from F Nadiya Nadiya

Can any one help me to clear whether the reference genome of related species or transcriptome of the same species is best for novel miRNA prediction?

I have my plant small RNA data from illumina. Done all quality filtration steps and conserved miRNA predictions. Now I have to predict novel miRNAs. In order to align, reference genome is not...

02 February 2018 3,720 8 View

Pathway analysis of denovo assembled transcriptome data using Plantcyc database?

Do any one have an experience in using plant cyc database? I have done the blastx of my assembled transcriptome with plantcyc.fasta file. The outfmt6 file generated shown some IDs only and no...

06 June 2016 5,039 6 View

Can i use more background references for miRNA target prediction?

We identified conserved and novel miRNA from my plant samples (non model plant). The targets were predicted through psRNA target using Arabidopsis as the background reference but targets were not...

03 March 2016 6,710 3 View

Do any one have an experience in running MIRA for denovo transcriptome assembly?

I ran MIRA with 1.2 GB (after pre processing) of my plant ion proton transcriptome data in a 120 GB RAM system. We are working through a rented server. Currently it is running and generated...

03 March 2016 1,558 4 View

How to perform pathway analysis for elucidating miRNA regulated pathways?

I have conserved and novel miRNAs of my plant samples and done the target prediction. Can any one please suggest me how could or any computational tools for analyzing the miRNA regulating pathways?

01 January 2016 9,732 9 View

Should I remove rRNAs from transcriptome data while moving on to Denovo assembly?

I have my transcriptome data of plant samples. Since the reference genome of my plant or its closest species is not available i have to go for denovo transcriptome assembly. Before assembly do i...

10 October 2015 7,201 7 View

Could any one help me in identification of novel miRNAs from plant species without a reference genome?

I am currently doing the NGS data analysis of miRNAs from my plant samples and after pre processing the reads were aligned against plant miRNAs from miRBase. In the proceeding step all paper...

09 September 2015 8,760 12 View

Can any one help me in flowcytometry histogram interpretation?

I am doing flow cytometry for the genome size determination of my plant samples. But the histograms obtaining every time is quite confusing.Is any one have an experience in plant flow cytometry...

06 June 2015 6,202 0 View