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Forum: RNA Sequencing 03-24-2015, 03:15 AM
Replies: 1
Views: 1,269
Posted By bob-loblaw
Gene prediction from RNA-Seq assembly

Hi all,

I've seen in a few different places that gene prediction is included as part of an RNA-Seq assembly analysis framework. But, in theory at least, shouldn't the contigs correspond to coding...
Forum: Bioinformatics 12-18-2014, 06:48 AM
Replies: 0
Views: 1,039
Posted By bob-loblaw
DESeq2 ntop set to 500?

Hi all,

I was just making some PCAs and I noticed that the plotPCA function within DESeq2 only takes the 500 genes with the highest variance. I was wondering if anyone knows what is the...
Forum: Bioinformatics 10-21-2014, 05:22 AM
Replies: 0
Views: 1,953
Posted By bob-loblaw
Common Dispersion in EdgeR

Hi all,

I had a question about the common dispersion in EdgeR. In the manual it gives the following..

> sqrt(d$common.disp)
[1] 0.416

The square root of the common dispersion gives the...
Forum: Bioinformatics 08-07-2014, 05:48 AM
Replies: 9
Views: 2,444
Posted By bob-loblaw
and yeah it comes from Arrested Development. Bob...

and yeah it comes from Arrested Development. Bob loblaws law blog :D

You know come to think of it, I have seen something like this in RNA-Seq datasets before, even published ones, where one...
Forum: Bioinformatics 08-07-2014, 01:46 AM
Replies: 9
Views: 2,444
Posted By bob-loblaw
Oh sorry my bad, that first sequence must be from...

Oh sorry my bad, that first sequence must be from some other source.

Well that's the problem, in some files its as high as 50%. I've had problems with contamination in this dataset before though...
Forum: Bioinformatics 08-07-2014, 12:59 AM
Replies: 9
Views: 2,444
Posted By bob-loblaw
Yeah the leftover reads are what I meant. The...

Yeah the leftover reads are what I meant. The quality varies a bit, there are some bad in there, but plenty of good too. But the quality on all of these reads should be enough to allow an accurate...
Forum: Bioinformatics 08-06-2014, 05:58 AM
Replies: 9
Views: 2,444
Posted By bob-loblaw
Bowtie2 detecting human transcripts that STAR misses

Hi everyone,

I'm having the problem mentioned in the title above and it's not making any sense to me. In the RNA-Seq dataset that I have I run STAR, then I look at the left over transcripts,...
Forum: Bioinformatics 01-16-2014, 12:27 PM
Replies: 1
Views: 2,190
Posted By bob-loblaw
RNA-Seq spliced aligners. Exon first vs Seed extend

Hi guys.

I was just wondering about some peoples opinions on RNA-Seq aligning methods. Maybe I'm misunderstanding it but I would think that seed extend aligners like STAR are inherently better,...
Forum: Bioinformatics 01-16-2014, 08:23 AM
Replies: 5
Views: 5,873
Posted By bob-loblaw
I wonder though in everyone's experience, what's...

I wonder though in everyone's experience, what's an "acceptable" percent of no features? Surely no organism's annotation is perfect? Plus how often is it that the RNA that you get is 100% mRNA

In...
Forum: Bioinformatics 01-15-2014, 05:53 AM
Replies: 8
Views: 3,212
Posted By bob-loblaw
Well I'm not too worried about 1.7 being...

Well I'm not too worried about 1.7 being overwritten, as long as 1.8 is fully functional. I'm just worried that it'll run into a problem and I'll be left with 2 half installed versions of QIIME,...
Forum: Bioinformatics 01-15-2014, 05:33 AM
Replies: 8
Views: 3,212
Posted By bob-loblaw
I haven't tried it, I'm not really sure how it'll...

I haven't tried it, I'm not really sure how it'll affect the installation of qiime already on the machine.
Forum: Bioinformatics 01-15-2014, 04:54 AM
Replies: 8
Views: 3,212
Posted By bob-loblaw
Ah thanks. Yeah it does come with bio-linux as...

Ah thanks. Yeah it does come with bio-linux as standard. Ah I see now, the built in packages with bio-linux can actually be updated through the normal ubuntu update manager, I think I already knew...
Forum: Bioinformatics 01-15-2014, 01:07 AM
Replies: 8
Views: 3,212
Posted By bob-loblaw
Upgrading qiime in bio-linux from 1.7 to 1.8

I was wondering if anyone had any experience with this? I know there is the qiime deploy script, which I'm going to try but I was hoping someone had some experience trying this.
Forum: Bioinformatics 07-30-2013, 02:49 AM
Replies: 0
Views: 1,203
Posted By bob-loblaw
RNA-Seq mapping to a genome vs transcriptome?

Hi All,


I'm currently looking at putting together a reference database for mapping my RNA-Seq reads and I was wondering what people think is the best way to go. I was thinking about mapping...
Forum: Bioinformatics 07-01-2013, 08:58 AM
Replies: 2
Views: 1,462
Posted By bob-loblaw
What proportion of 'bad' quality reads are expected using HiSeq 2000 for RNA-Seq

I am just after processing 24 files, using trimmomatic to quality filter them. On average was 30% of the reads were bad quality (SD = 11).

This seems somewhat high to me, I was just wondering if...
Forum: Bioinformatics 06-26-2013, 01:07 AM
Replies: 20
Views: 14,366
Posted By bob-loblaw
Well I've never felt as stupid as I do right now...

Well I've never felt as stupid as I do right now haha. Thanks though!
Forum: Bioinformatics 06-25-2013, 02:51 AM
Replies: 20
Views: 14,366
Posted By bob-loblaw
Here is the log file from one where the...

Here is the log file from one where the introMotif option does not work! Thanks!
Forum: Bioinformatics 06-17-2013, 08:18 AM
Replies: 1
Views: 1,257
Posted By bob-loblaw
Best way to find host organism for protein IDs

Hello,

I inherited some bioinformatics RNA-Seq from someone else, and I'm trying to make sense of something that they did. The project was looking for differentially expressed genes using DESeq,...
Forum: Bioinformatics 06-15-2013, 09:06 AM
Replies: 20
Views: 14,366
Posted By bob-loblaw
The unmapped fastx is working for me now as is...

The unmapped fastx is working for me now as is cufflinks, it started working with the version I had installed though. Odd. Although I've noticed with the intronmotif option for cufflinks that it only...
Forum: Bioinformatics 06-13-2013, 06:40 AM
Replies: 20
Views: 14,366
Posted By bob-loblaw
I've had issues with this version of STAR on my...

I've had issues with this version of STAR on my machine before. The option for writing out unmapped reads to fastq format doesn't work either, although theres a pretty easy workaround for that. I may...
Forum: Bioinformatics 06-13-2013, 05:47 AM
Replies: 20
Views: 14,366
Posted By bob-loblaw
Hi guys, this is probably a good place to...

Hi guys,

this is probably a good place to ask this question. But I ran STAR with that option to add the XS attribute. But when I run cufflinks I get this

BAM record error: found spliced...
Forum: Bioinformatics 05-31-2013, 05:52 AM
Replies: 0
Views: 2,222
Posted By bob-loblaw
Error with RSEM/eXpress/cufflinks

Hi All! Hopefully someone can help me here, I'm trying to quantify expression from bowtie2 output.
When I try to used RSEM/eXpress, it fails because it detects that there is something in the header...
Forum: Bioinformatics 05-31-2013, 05:46 AM
Replies: 21
Views: 7,978
Posted By bob-loblaw
Well alternatively spliced genes won't be a...

Well alternatively spliced genes won't be a problem, it's all bacteria I'm mapping to. RSEM I have been playing around with, but I have a pretty large sample size, and realigning all of them would be...
Forum: Bioinformatics 05-29-2013, 09:17 AM
Replies: 21
Views: 7,978
Posted By bob-loblaw
I'll look into it. Thank you.

I'll look into it. Thank you.
Forum: Bioinformatics 05-29-2013, 09:07 AM
Replies: 21
Views: 7,978
Posted By bob-loblaw
Ah okay. I misunderstood, I thought sdriscoll was...

Ah okay. I misunderstood, I thought sdriscoll was asking if I was mapping against a reference assembled from transcriptomics data, as opposed to the DNA sequences of predicted proteins from sequenced...
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