Questions tagged [non-coding]

This refers to parts of or whole transcripts (or occasionally genes) that are not translated into proteins.

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Statistical methods suitable for DE analysis of non coding RNAs

I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package. Is the negative binomial method that is ...
Arkajyoti Banerjee's user avatar
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Are there databases to annotate non-coding mutations?

I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome? Preferably, if the database is downloadable so I am able to ...
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Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?

I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions. I was looking for GATK best practices (like ...
gc5's user avatar
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Filtering criteria for non-coding features with very low counts

I am trying to do DE analysis of non-coding features of A. thaliana. I find in the miRNA and lncRNA counts file that they are abundant in zero counts, and most of the non-zero counts are very low. Now,...
Arkajyoti Banerjee's user avatar
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using Bowtie to map miRNA-seq data to rfam and also reference genome

I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code: ...
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Target genes for piRNA

Where I can find a database or tool to give me the target genes of PIWI (piRNAs) in human? I found one but works for worm like <...
Zizogolu's user avatar
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Is is possible to predict ncRNAs from sequence and homology alone?

I'm working with a set of homologous genes (let's call it gene A) from several bacterial species. I know (from previously published research) that in gene B (a close paralogue of gene A), there is a ...
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