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Search: Posts Made By: tirohia
Forum: Bioinformatics 09-26-2017, 06:31 PM
Replies: 1
Views: 2,571
Posted By tirohia
removing chromosomes from a bam file.

I'm trying to upload a bam file, from an alignment to GRCh38 that I've done, to a google genomics dataset, associating it with the reference set for GRCh38. The reason it fails given in the logfile...
Forum: RNA Sequencing 09-11-2017, 01:07 PM
Replies: 5
Views: 1,878
Posted By tirohia
Is there a formal bug submission process (if so I...

Is there a formal bug submission process (if so I can't find it), or does one just submit a new issues via github?
Forum: RNA Sequencing 09-10-2017, 06:24 PM
Replies: 5
Views: 1,878
Posted By tirohia
So when I run an alignment with bowtie2, it takes...

So when I run an alignment with bowtie2, it takes maybe an hour or. When I do it with Hisat2, it'll run for days.

I've been logging the CPU usage with:
while true; do (echo "%CPU %MEM ARGS...
Forum: Bioinformatics 09-09-2017, 11:53 PM
Replies: 0
Views: 783
Posted By tirohia
Hisat2 multithreading not working.

As best I can see, this should be working. I've got 16 cores:

$ grep -c ^processor /proc/cpuinfo
16


I then attempt to use hisat2 with multiple threads. I've tried using both --threads...
Forum: RNA Sequencing 09-09-2017, 11:30 PM
Replies: 5
Views: 1,878
Posted By tirohia
Hisat2 multithreading not working.

As best I can see, this should be working. I've got 16 cores:

$ grep -c ^processor /proc/cpuinfo
16


I then attempt to use hisat2 with multiple threads. I've tried using both --threads...
Forum: Bioinformatics 08-06-2017, 05:21 PM
Replies: 0
Views: 628
Posted By tirohia
Too many samples

So I've been given transcriptome data for ... quite a lot of samples (>500). It's all from various tumours from one specific tumour type. There's a clinical grading for how serious each tumour is.
...
Forum: Bioinformatics 05-31-2017, 05:34 PM
Replies: 4
Views: 1,129
Posted By tirohia
I'm not just starting out. I used the exact same...

I'm not just starting out. I used the exact same pipeline to process a timcourse about a year-ish ago - one of the reasons I was thinking that the gtf/genome files, as you say, might not be matching....
Forum: Bioinformatics 05-29-2017, 08:43 PM
Replies: 4
Views: 1,129
Posted By tirohia
No counts from HTSEq

So I've just used the pre-built GRCh38 bowtie2 index to map paired end reads using Tophat. Approximately 70% of the reads mapped (~11000000).

tophat -o pilot_S10.5...
Forum: Bioinformatics 05-20-2017, 04:18 PM
Replies: 4
Views: 1,651
Posted By tirohia
I was about to post on exactly the same topic -...

I was about to post on exactly the same topic - I've got two peaks, one quite sharp in the GC content across all 12 samples in an experiment. As best I can tell from googling is that contamination is...
Forum: Bioinformatics 10-31-2016, 05:12 PM
Replies: 0
Views: 882
Posted By tirohia
gene ratios across RNASeq/amplicon datasets

Say you have one set of data that is derived from isolating certain transcripts and amplifying them. And another set of data that consists of RNASeq of the entire transcriptome.

Would you expect...
Forum: Bioinformatics 02-23-2016, 04:44 PM
Replies: 5
Views: 1,202
Posted By tirohia
Thanks Geno - I've managed to get something sort...

Thanks Geno - I've managed to get something sort of close to what I'm trying to do out of bedtools - I should have thought of that.

Michael - I'm actually looking for areas with no annotation...
Forum: Bioinformatics 02-19-2016, 06:48 PM
Replies: 5
Views: 1,202
Posted By tirohia
Count reads mapping to non-feature area

I have a bam file containing arabidopsis short RNA reads that I have mapped to the TAIR10 genome. Is there an easy way to get counts of reads that overlap each other and the corresponding...
Forum: Bioinformatics 01-04-2016, 07:52 PM
Replies: 1
Views: 866
Posted By tirohia
Others may correct me if I'm wrong, but I've...

Others may correct me if I'm wrong, but I've always understood that to be yes, there might exist an alignment with a better score. It finds the best alignment it can given the constraints on it -...
Forum: Bioinformatics 10-23-2015, 11:06 PM
Replies: 0
Views: 1,035
Posted By tirohia
Strange dispersion estimates from DESeq

I'm just starting on a new time series dataset (last one for the phd!). There's something odd in happening with the dispersion estimates though. It's something in my data doing this rather than...
Forum: Bioinformatics 08-16-2015, 09:51 PM
Replies: 1
Views: 452
Posted By tirohia
collapsing multiple genes into a meta-gene.

The end goal is to cluster some time series data.

Using multiple different methods, I've identified a number of differentially expressed genes over a timecourse.
I've got two possible sets of...
Forum: Bioinformatics 08-10-2015, 08:40 PM
Replies: 1
Views: 1,178
Posted By tirohia
EdgeR TMM normalization with the glm model

So I've had edgeR running on some time course data. When comparing any two samples using a basic edgeR analysis, I include the line

y <- calcNormFactors(y)

in my pipeline. I note that this...
Forum: Bioinformatics 06-17-2015, 12:54 AM
Replies: 0
Views: 1,212
Posted By tirohia
EdgeR test for differential expression.

I'm reading the Robinson and Smyth's 2008 paper: Small-sample estimation of negative binomial dispersion, with applications to SAGE data

Wondering if anyone can clarify the final test being used...
Forum: Bioinformatics 06-16-2015, 06:04 PM
Replies: 4
Views: 1,668
Posted By tirohia
help(nbinomWaldTest) appears to be a much more...

help(nbinomWaldTest) appears to be a much more succinct summary of the paper. It helps, thanks.

Now that you mention it, I do recall the DESeq2 manual somewhere saying that uses the first factor...
Forum: Bioinformatics 06-15-2015, 04:36 PM
Replies: 4
Views: 1,668
Posted By tirohia
Okay. That makes sense. Thanks. A further...

Okay. That makes sense. Thanks. A further question if I may though.

The definition of βir provided is the LFC for gene i, covariate r. Does this mean that βir is the LFC between the replicates...
Forum: Bioinformatics 06-15-2015, 01:07 AM
Replies: 4
Views: 1,668
Posted By tirohia
Question about DESeq2 LFC shrinkage estimation.

Currently working my way through the paper: Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2 courtesy of Love, Huber and Anders.

In the model specification, in...
Forum: Bioinformatics 02-25-2015, 03:20 PM
Replies: 5
Views: 1,428
Posted By tirohia
Sarvidsson - bacterial reads from the time course...

Sarvidsson - bacterial reads from the time course samples, yeah, I've got tens of thousands. The plant reads have taken up most of the space. When I designed the experiment all the biologists thought...
Forum: Bioinformatics 02-24-2015, 08:24 PM
Replies: 5
Views: 1,428
Posted By tirohia
Differential expression between samples from different experiments

I have some RNASeq data from a time course experiment that is a mix of (mostly) plant and bacterial reads. I have a senior scientist (I'm a phd student) who has approached me asking me to do a...
Forum: Bioinformatics 01-15-2015, 07:39 PM
Replies: 6
Views: 2,991
Posted By tirohia
Ahh... that light dawns. :) Thanks for the...

Ahh... that light dawns. :)

Thanks for the link. I think I've got it all sorted in my head now.

Also, I've just noticed that when I was filtering on the lfc in edger I was filter on lfc>2 and...
Forum: Bioinformatics 01-14-2015, 05:48 PM
Replies: 6
Views: 2,991
Posted By tirohia
I'm assuming that plotMA() will plot using the...

I'm assuming that plotMA() will plot using the lfcMLE if it's present over the log2FoldChange?

So in edgeR, to get those 3200 DE genes, I'm using the test, which, as you point out is testing that...
Forum: Bioinformatics 01-13-2015, 02:34 PM
Replies: 6
Views: 2,991
Posted By tirohia
Apologies, that was a copy/paste error on my...

Apologies, that was a copy/paste error on my part.
The DESeq comparisons that I've made are:
results <- results(dds,contrast=c("condition","Control","Psa"), lfcThreshold=2,...
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