Which is the best tool for analyze DNA-seq data From ITS region (Where Can We found a good library fro the aligment)?

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Have anyone experience about the effect of time in the expression of CircRNA?

We have some experience in different splicing in some RNA depending of the time that the blood is in the bench waiting for the RNA extraction. We are wondering if that can occurs also with circRNA.

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Which is the correct percentage of Ethanol in the TRIZOL-RNA extraction to recover the small RNA?

Technical question about the RNA extraction with TRIZOL

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Does anyone has an idea about the coverage needed to study CircRNA in RNA( enriched in circRNA by rRNA depletion and RNASe R enrichement) from PBMC?

How coverage will I need in a NGS study to cover all circRNA? The sample will be RNA from PBMC, previously treated with rRNA depletion and RNAse R (to enrich the sample in circ)

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Anyone know how to correct batch effect in microarray expression data using BRB Array tools?

Batch effect in two datasets of HUgene Affymetrix arrays.

03 April 2013 3,767 1 View

We have some troubles with the identification of C9orf72 expansion by PCR. Has anyone a better way to detect it?

C9orf72 is an expansion related to some neurological diseases such as ALS or dementia.

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Where to find a gene list for CRISPRa/i library screening of regulatory factors that affect pathogenic Th17 differentiation in PBMC?

I want to perform a CRISPRa/i library screening for candidate regulatory factors that affect pathogenic Th17 differentiation in PBMC. But I am wondering how to define the size of gene library, so...

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How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 View

Which software tools are best for enhancing diagnostic accuracy in chest X-ray imaging using image reconstruction and neural networks?

I am reaching out to seek your valuable advice and recommendations regarding the best software tools to use for this research. Specifically, I am looking for software with a user-friendly...

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How to fix install package meta in R?

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I want to conduct a research using quasi experimental design to test two treatment and one control what type of statistical tools do l use ?

What type of experimental design do l use and what statistical tools do l use for the hypothesis. What is the position of control group in the analysis?. Thanks

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Which research tool for expert validation for our study?

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Figure plot in scientific articles?

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Can it is possible to find the cleaved sequence when a protein cleaved by a heamaglutanin protease (HA/P) by any bioinformatics tools?

Bioinformatics tools like peptide cutter

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What is the difference between OTU and ASV analysis?

For microbiome data analysis

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How to predict Shine-Dalgarno sequence ?

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Frederic Lepretre

Hi David,

here is a track you can follow (Article Improved software detection and extraction of ITS1 and ITS2 ...

)

fred

Waqar Ahmad

I am also struggling with the answer. However, I used GALAXY for file conversions that helped me a lot. I am using GALAXY tools as well IVG for data analysis.

Rana Khayat

I have used BLAST at GenBank

David Otaegui

Thanks Rana, but the question, coming from DNAseq data is which is the best bam file to do the aligment (In the same way of what we do for 16S gene)

Ferdinando Bonfiglio

Hi David!

I suggest you to use this database: http://itsonedb.cloud.ba.infn.it and a mapping tool like bwa if you have short reads or minimap2 in case of long reads.

Thanks Nando!!!