We have obtained the NGS small RNA sequencing Raw reads (Outsourcing) How to check the sequence integrity?

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Facing difficulty in isolation of complete CDS of selected gene?

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Which package is better for calculate DE genes?

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How to prepare a Micro RNA probe (manual) for Northern blotting?

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Is there a problem with my RNA pellet?

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Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

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Strugglling with m6A dot blot any suugesstion ?

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How to confirm the site-directed mutagenesis result without performing NGS?

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RNA Extraction Using Hot Borate Method No Longer Working?

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Does Anyone have expertise in in vitro transcription and RNA pull down assay?

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E.coli contamination in human RNA seq data ?

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RNA later for the preservation of RNA in fecal samples at room temperature for one day (37°C)?

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Do you have good tips for seaweed tissue preservation in the field for post RNA extraction?

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Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

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Ashwani Jha

Hi, you can use NGSQC toolkit (http://www.nipgr.res.in/ngsqctoolkit.html) or fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)

Hemant Gupta

@Ashwani Jha, well suggested! I would like to add one more (highly cited) tool in the list and that is FastQC.

After quality check you can filter your data using cutadapt (widely used for small RNA data filtration) & Trimmomatic.

Hope this helps!

Gina Pham

I also suggest FastQC. FastQC will give you an easy to read HTML report so you can see quality along read, contamination from adapters, etc.

Adita Joshi

I agree with Gina and hemant

Ellango Ramasamy

Thanks for all.

Actually I want to remove other snRNA like piRNA tRNA etc along with the adaptors and other in the small RNA transcriptome data. Is it possible in cutadapt? or I want to write any script.