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11 votes
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What to use to edit RNA alignments?

I would suggest use RALEE—RNALignment Editor in Emacs. It can get for you the consensus secondary structure, you can move left/right sequences and their secondary structures (you can't do it in ...
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11 votes

Why does the SARS-Cov2 genome has letter t

We sequence and therefore typically report assemblies as DNA sequences, even if they're actually RNA.
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8 votes
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How to extract RNA sequence and secondary structure restrains from a PDB file

I suggest you take a look at rna-pdb-tools we do way more than you need! :-) The tools can get you a sequence, secondary structure and much more using various ...
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7 votes

What to use to edit RNA alignments?

There's nothing really special about RNA alignments, you can use any alignment editor, including whichever one you use for protein. That said, a classic and very useful tool for this sort of thing is ...
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  • 7,957
7 votes
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5' and 3' bias in Rna-seq data

I expect there was a sequencing problem during the last base, where some of the reagents were running low on the sequencer. This won't pose any real problem, RNAseq aligners like STAR will just soft-...
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6 votes

Basic questions about GSEA

Use the following R package for Gene Set Enrichment analysis of RNA-seq data: seqGSEA There is another R package (fgsea) recently published called "Fast Gene Set Enrichment Analysis" by Alexey ...
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  • 584
6 votes

Basic questions about GSEA

You seem to refer to the GSEA provided by the Broad institute, (there are other GSEA algorithms). 1) You can provide whatever you wish, but if you want to know if those gene sets in which side of ...
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  • 4,622
6 votes

How to filter ribosomal RNA from scRNA-seq data

In the paper mentioned, we used the ScaleData function in Seurat to regress out the number of reads, Rn45s abundance, and percent ribosomal gene transcripts. ...
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5 votes
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Why is ribosomal RNA difficult to remove even with Poly(A) selection?

We've found ribosomal RNA to be less of a problem with sequencing that depends on polyA, which suggests the issue might be in the library preparation, rather than the selection. Many polyA RNA ...
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4 votes

How to extract RNA sequence and secondary structure restrains from a PDB file

Context The PDB file format is a fixed-column file format designed in 1970s for storing structural models of macromolecules. The format has been around for long time, has many uses, and although it ...
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  • 1,036
4 votes

Estimate the length of poly-A tails from randomly-primed RNAseq data

Can’t be done. If you already sequenced then I’m afraid the money is wasted (unless of course the data is good for something else). The standard Illumina basecaller doesn’t deal well with ...
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4 votes

Detecting differentially expressed genes with foldchange >= 2 and FDR < 0.05

The edgeR authors recommend that you use a relatively low logFC threshold for glmTreat such as lfc=log2(1.2). A ...
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4 votes

How to convert featureCounts to FPKM?

I have seen many posts regarding counts to RPKM and TPM. There’s your answer then: FPKM = RPKM. It’s simply a more accurate name. Speaking of RPKM for paired-end data is discouraged because the ...
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4 votes

Why the t-test for a specific gene shows different value compared to differential analysis?

There is no reason your t-test should reproduce edgeR. In fact, edgeR exists because t-test is inappropriate. edgeR does the tests by pooling information from all genes, because with the low number ...
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4 votes
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Question about Co-expression analysis and finding targets for lncRNAs

You have several options to approach this with WGCNA (weighted correlation network analysis). You can run a WGCNA on the combined set, identify modules and select those lncRNAs for further follow-up ...
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3 votes
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Detecting differentially expressed genes with foldchange >= 2 and FDR < 0.05

Fold-change >= 2 is the same as logFC (log2(fold-change)) >= 1, so your example is doing exactly what you want. logFC is generally easier to think in and work with ...
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3 votes

Strange per sequence GC content results

Although generally I recommend people to be wary about the warnings that FastQC gives (it tends to be overly paranoid), the GC content graphs here do look odd. It's good that you've had a look at it ...
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3 votes

Reads mapped to exonic, intronic and intergenic regions

As @DevonRyan mentioned, it's very likely that those samples were degraded, which is good justification for excluding them from subsequent analysis.
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3 votes

How to calculate logCPM across all samples?

If you want the values by group then subset y to contain the samples of interest and then feed that to aveLogCPM().
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3 votes
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Estimate the length of poly-A tails from randomly-primed RNAseq data

Just look for polyA tracts at the end of sequences, and count them if they're larger than ~18 bases. I've done this with MinION cDNA reads by mapping the polyA adapter sequence (with an elongated ...
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3 votes
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How to filter ribosomal RNA from scRNA-seq data

The rRNA genes in that dataset are Rn45s and Rn4.5s. BTW, you have gene counts, not transcript counts.
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3 votes
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How to compute the chance of failing to detect a gene given the detection limit of a protocol

A 90% loss can be rephrased as a 10% chance of detecting anything. So what we want to find is the probability of detecting 0 molecules, when we start with 7 and have 10% probability of success. Once ...
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3 votes
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How can I dock a protein to a nucleic acid?

I'm not sure what you meant but you can take a look at NPDock (disclaimer we wrote that tool). If you have a structure of your protein of interest, you can dock it to the structure of your DNA/RNA of ...
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3 votes
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Selection of differential expressed genes

You can usually get away with FDR < 0.1, but that's as high as you can go. This all presumes you're doing follow-up experiments of some sort, of course. I guess you could increase the FDR more, but ...
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3 votes
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Why the t-test for a specific gene shows different value compared to differential analysis?

The $log(CPM)$ of any low-moderately expressed gene will be negative. There is nothing unexpected there. Your statistics are inappropriate for a variety of reasons. Firstly, a CPM is not a robust ...
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3 votes

Real time transcript profiles

Answer: There are no methods that exist for investigating transcript data inside a cell without destroying the cell. Separating RNA from cells requires essentially destroying the cells and using a ...
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3 votes
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Building RNAz on MacOS

Compile with gcc or remove inline from librna/fold.c:776 and librna/fold.c:846.
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  • 5,645
3 votes
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How to select only RNA with Hetero atoms from pdb file with python?

Solution I found: (c/p of body) ...
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3 votes

Practical use of RNA structure

Please look up flavivirus 'double loops' as you described them previously (post for "Coronavirus RNA') and associated RNA secondary structure anomalies for dengue virus and associated vaccine (...
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3 votes

Coronavirus RNA structures?

To add a more complete answer: the current coronavirus is closely related to the SARS virus that caused the outbreak in 2004, and on which much research has been done. Here is a general review of the ...
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