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Search: Posts Made By: dpryan
Forum: Bioinformatics 10-17-2017, 02:39 PM
Replies: 1
Views: 179
Posted By dpryan
Yes, most methylation is symmetric, I haven't a...

Yes, most methylation is symmetric, I haven't a clue why they're always getting such large differences between strands.
Forum: Bioinformatics 10-15-2017, 11:29 PM
Replies: 1
Views: 260
Posted By dpryan
I've had pretty good luck getting support...

I've had pretty good luck getting support directly from Illumina for issues like this, you might contact them and send the logs.
Forum: RNA Sequencing 09-11-2017, 11:10 PM
Replies: 5
Views: 523
Posted By dpryan
Github is usually as formal as things get, so...

Github is usually as formal as things get, so yes, post it there.
Forum: Bioinformatics 09-11-2017, 12:27 AM
Replies: 4
Views: 352
Posted By dpryan
How's your C programming? I suspect you're going...

How's your C programming? I suspect you're going to have to code something with htslib to figure out (A) where the problem is and (B) get around it as best as possible.
Forum: RNA Sequencing 09-11-2017, 12:20 AM
Replies: 5
Views: 523
Posted By dpryan
Please report this as a bug to the developers. I...

Please report this as a bug to the developers. I should note that it runs multithreaded for us, so there's some odd interaction between the binary and your system.
Forum: Bioinformatics 08-11-2017, 01:53 AM
Replies: 1
Views: 361
Posted By dpryan
Usually it's the mean of all samples.

Usually it's the mean of all samples.
Forum: Sample Prep / Library Generation 08-09-2017, 01:43 AM
Replies: 3
Views: 607
Posted By dpryan
The first question to ask is whether this is...

The first question to ask is whether this is really a problem with the library or instead one of the aligner or its settings. What are you using there?
Forum: Bioinformatics 08-01-2017, 11:20 PM
Replies: 2
Views: 630
Posted By dpryan
The base qualities for the whole file are summed...

The base qualities for the whole file are summed and then that's divided by the total number of bases in the file.
Forum: Bioinformatics 07-24-2017, 10:45 PM
Replies: 3
Views: 4,894
Posted By dpryan
Post it in a new thread rather than reviving one...

Post it in a new thread rather than reviving one from 6 years ago.
Forum: Bioinformatics 07-02-2017, 10:33 PM
Replies: 8
Views: 706
Posted By dpryan
1. Run featureCounts to produce counts. 2. Load...

1. Run featureCounts to produce counts.
2. Load into DESeq2 or edgeR or limma and follow the appropriate vignette

Salmon is a newer method that requires either fastq files or BAM files of...
Forum: General 06-22-2017, 12:02 AM
Replies: 1
Views: 540
Posted By dpryan
I've answered your identical post on biostars...

I've answered your identical post on biostars (https://www.biostars.org/p/259076/).
Forum: Bioinformatics 06-21-2017, 11:56 PM
Replies: 2
Views: 276
Posted By dpryan
Yes, you must index the BAM file too.

Yes, you must index the BAM file too.
Forum: Pacific Biosciences 06-01-2017, 11:54 PM
Replies: 2
Views: 534
Posted By dpryan
The absolute minimum is 3 per group. The "pilot"...

The absolute minimum is 3 per group. The "pilot" request is presumably due to the fact that an n of 64 is well within the range of a pilot study for clinical trials. Presuming you're not doing a...
Forum: Academic/Non-Profit Jobs 04-26-2017, 11:16 PM
Replies: 2
Views: 662
Posted By dpryan
I went from neuroscience -> bioinformatics, so...

I went from neuroscience -> bioinformatics, so perhaps I can provide some insight.

As a general rule, if you're interested in pursuing a career as an analyst and can get a job with your current...
Forum: Complete Genomics 04-22-2017, 02:05 PM
Replies: 6
Views: 1,320
Posted By dpryan
I thought BWA (as ends up being the case with a...

I thought BWA (as ends up being the case with a lot of aligners) ends up concatenating the chromosomes together when indexing (with a bunch of N in between). Anyway, BWA at least used to occasionally...
Forum: Bioinformatics 04-04-2017, 01:34 AM
Replies: 4
Views: 568
Posted By dpryan
My guess (since I haven't a clue about the...

My guess (since I haven't a clue about the background to your experiment) is that you want vpu="Wt" for the mock infected samples. The combination of vpu and virus would then be distinct.

*Edit*:...
Forum: Bioinformatics 04-04-2017, 12:08 AM
Replies: 4
Views: 568
Posted By dpryan
The problem is that "virus==none" is the same as...

The problem is that "virus==none" is the same as "vpu==mock".
Forum: Bioinformatics 04-03-2017, 11:50 PM
Replies: 4
Views: 734
Posted By dpryan
The presumption is that the p-value is from a...

The presumption is that the p-value is from a poisson test, so yes it's between the two samples.

Yes, p<0.05 would normally mean differentially expressed, aside from the fact that the p-values in...
Forum: Bioinformatics 04-03-2017, 01:10 AM
Replies: 4
Views: 734
Posted By dpryan
If you only sent them single samples from your...

If you only sent them single samples from your groups then the p-values are largely meaningless. There's not a direct correspondence between fold-change and p-value, since lowly expressed genes will...
Forum: Illumina/Solexa 03-29-2017, 06:15 AM
Replies: 4
Views: 851
Posted By dpryan
We usually get 300-400 million passing filter per...

We usually get 300-400 million passing filter per lane on a HiSeq3000. "Optical" duplicates are typically below 10%, except with weird library types. Often the higher the read yield the lower the...
Forum: Bioinformatics 03-14-2017, 12:33 AM
Replies: 8
Views: 580
Posted By dpryan
Compare that to the (generally superior) Ensembl...

Compare that to the (generally superior) Ensembl annotation. KRAS in refgene is 46143, in Ensembl (even back in hg19) it's 46148. The just differ by some (likely intronic) indels.

Anyway, genes in...
Forum: Bioinformatics 03-13-2017, 07:36 AM
Replies: 8
Views: 580
Posted By dpryan
It's likely that you're looking at the length of...

It's likely that you're looking at the length of the gene in one case and the length of the spliced transcript in the other.
Forum: Bioinformatics 03-13-2017, 03:07 AM
Replies: 4
Views: 379
Posted By dpryan
Exactly, you'd need to store the gene_id to...

Exactly, you'd need to store the gene_id to position association somewhere.
Forum: Bioinformatics 03-13-2017, 02:45 AM
Replies: 4
Views: 379
Posted By dpryan
It won't accept that at all. You will need to...

It won't accept that at all. You will need to convert that to a genomic range.
Forum: Epigenetics 03-13-2017, 01:05 AM
Replies: 1
Views: 747
Posted By dpryan
"Alignment Dichte", to make up a phrase in...

"Alignment Dichte", to make up a phrase in quasi-German. The reads/alignments are from the sequencing data, the density simply refers to how many are in a particular area. In this case, it's...
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