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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 ...
Marcin Magnus's user avatar
10 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.
Devon Ryan's user avatar
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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 ...
Marcin Magnus's user avatar
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 ...
terdon's user avatar
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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-...
Devon Ryan's user avatar
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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 ...
arup's user avatar
  • 594
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 ...
llrs's user avatar
  • 4,662
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. ...
Olga Botvinnik's user avatar
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 ...
gringer's user avatar
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5 votes
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Gene symbol list for all protein coding genes in mice

If you want all known mouse protein coding genes, you can get the list from Ensembl's BioMart. First, select the mouse genome: Then, in "Filters" limit to protein coding genes only: And ...
terdon's user avatar
  • 9,352
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 ...
marcin's user avatar
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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 ...
Konrad Rudolph's user avatar
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 ...
Konrad Rudolph's user avatar
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 ...
ABCD's user avatar
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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 ...
Peter Langfelder's user avatar
4 votes

How to calculate the Maximum Ladder Distance (MLD) of ssRNA from Dot-Bracket notation?

There are different implementations for calcuating the $\rm MLD$. One possible approach is to consider $\rm MLD$ as the heighest value of all possible mountain plots, generated by shifting the ...
Domen's user avatar
  • 141
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().
Devon Ryan's user avatar
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3 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 ...
Gordon Smyth's user avatar
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 ...
Devon Ryan's user avatar
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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 ...
gringer's user avatar
  • 13k
3 votes

5' and 3' bias in Rna-seq data

I know this is an old post, but if this plot is from after trimming I would suggest a different explanation: some trimming tools remove poly-A sequences from reads. If that's the case then any read ...
ewels's user avatar
  • 291
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.
Daniel Standage's user avatar
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 ...
gringer's user avatar
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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.
Devon Ryan's user avatar
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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 ...
Devon Ryan's user avatar
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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 ...
Marcin Magnus's user avatar
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 ...
Devon Ryan's user avatar
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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 ...
Devon Ryan's user avatar
  • 19.5k
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 ...
conchoecia's user avatar
  • 3,111
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.
user172818's user avatar
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