Questions tagged [rna]

Use this tag to refer questions that are related to rna sequence.

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Parse RNA variant effect annotations (“r.” format)

I've got annotations for splicing variants in a format like this (this is one variant): Variant: NM_004092.3:c.88+5G>A Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23) I want to extract ...
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68 views

How is that ensemble Free energy is lower than the MFE in RNAfold from ViennaRNA

In the tutorial of RNAfold it states, RNAfold reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in ...
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1answer
93 views

How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in ...
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39 views

Can someone explain how this algorithm describes RNA folding to me in terms of what each symbol & value represents?

I need someone to explain to me from the nuts and bolts how algorithms/ maths is used to work out RNA folding. Explain it to me like I am an alien, or a child, an alien-child. I am looking at this ...
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0answers
85 views

How to correctly parallelise RSeQC scripts with GNU parallel?

I have a .bam, as ouput from STAR aligner, from which I need to extract some info using RSeQC while using all the computational resources available to increase ...
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105 views

How to create a SAF file for virus sequence?

I am trying to create a SAF file for the virus sequence. I can download .gff3 and .gb format for the virus gene sequence but they are not supported by featureCounts. I need to create my own SAF. I ...
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1answer
40 views

How to count RNA sequencereads using custom made python scripts?

I am trying to do RNA seq analysis and my goal is to filter gene counts less than 5 using custom made python scripts. The code chunk goes as follows ...
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10 views

RNA loop prediction: how to interpret differences between RNAfold and Mfold?

I'm trying to find out the structure of a conserved ITS loop. As my initial prediction (using only bases homologous to those present in the loop in a closely-related species) was fairly low-scoring, I ...
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18 views

Detecting Transcript Isoforms with HISAT2/Stringtie RNAseq Output

I have the following Stringtie RNA-seq output files for several samples in the image below. For additional context, I have utilized as part of my RNA-seq workflow. HISAT2, samtools, and Stringtie ...
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84 views

about the scaling after normalization and transformation in RNA-seq data

When we use count data in RNA-seq analysis, we usually use normalization and sometimes vst, rlog transformation (DESeq2)or log2(CMP+4) transformation (edgeR) to perform K-means clustering. Can we use ...
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1answer
51 views

Tool for rna/lna melting temperature prediction

Is there any tool available to predict the melting temperature for rna/lna oligos with its perfect complement ? I know this amazing website from qiagen/geneglobe that estimates the tm value. But ...
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24 views

What are the meanings of these transcript ids?

I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser. ...
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15 views

Arm-level SCNA does not change mRNA expression level?

It is almost common sense that local amplification of gene increase the its mRNA expression . I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA ...
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1answer
147 views

How to handle control samples in CLIP-Seq

I have a CLIP-Seq dataset I'm processing, which includes control samples and no inputs. This is the second CLIP analysis I've performed to help out users of our genome core facility and the first one ...