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Forum: SOLiD 03-27-2020, 09:39 AM
Replies: 3
Views: 6,302
Posted By samhokin
Hey, the data turned out OK and was useful! But...

Hey, the data turned out OK and was useful! But yeah, I had to dust off the hard drive the reads were on, it'd been sitting on a shelf for eight years or so. :)
Forum: Bioinformatics 03-06-2020, 02:42 AM
Replies: 0
Views: 636
Posted By samhokin
Question bcftools call: why is this a 1/1?

I can't for the life of me figure out why bcftools call genotypes this position (and many, many others like it) as 1/1:

Here's the input VCF line:
...
Forum: SOLiD 06-24-2019, 07:21 AM
Replies: 3
Views: 6,302
Posted By samhokin
What are these BC files for? Should I use them in alignment?

Hi, folks. I've started working with some old SOLiD single-ended RNA-seq reads, from 2010 and 2011. I'm using novoalignCS and have the quality files, csfasta files, and an additional fasta-like file...
Forum: Bioinformatics 08-11-2017, 01:42 PM
Replies: 21
Views: 20,331
Posted By samhokin
Same here, the bcftools that is compiled within...

Same here, the bcftools that is compiled within samtools is old, and when I compiled a fresh version from github, this error vanished.
Forum: Bioinformatics 10-03-2016, 02:58 PM
Replies: 2
Views: 1,509
Posted By samhokin
As I understand it, MEME defaults to NOT finding...

As I understand it, MEME defaults to NOT finding motifs on opposite strands. Use the -revcomp parameter to have MEME search the reverse strand as well.
Forum: RNA Sequencing 05-31-2016, 01:50 PM
Replies: 0
Views: 1,042
Posted By samhokin
Tophat2 chose a match with a deletion over one without

I'm a bit mystified by Tophat's (v2.1.0) choice of alignment in a case where I've got two similar genomes placed end to end (B73 and W22 maize) and I'm trying to map reads from a mixed (or non-mixed...
Forum: Bioinformatics 12-30-2015, 09:39 AM
Replies: 1
Views: 1,632
Posted By samhokin
Can anyone help me with this? Now I'm having the...

Can anyone help me with this? Now I'm having the same result when I try to map single-fastq reads (multplexed-PE in this case) to the Maize AGPv3 genes. Run-of-the-mill application of TopHat2. Here's...
Forum: RNA Sequencing 04-02-2015, 09:51 AM
Replies: 0
Views: 1,351
Posted By samhokin
Extra high-count repeats in small RNA reads

I'm new to small RNA sequencing, and a bit confused about some of the sequences I'm seeing and wonder if you can provide some tips. I'm looking at a public dataset (SRP032955) in which the reads have...
Forum: Bioinformatics 12-30-2014, 02:59 PM
Replies: 1
Views: 1,632
Posted By samhokin
Tophat2 never completes Generating SAM header

I think this has been touched upon before, but I haven't been able to find a definitive answer, so here I go. Apologies if previously addressed.

I'm trying to map single-ended RNA-seq reads...
Forum: RNA Sequencing 04-05-2014, 05:47 AM
Replies: 8
Views: 7,552
Posted By samhokin
Mine are actually independent bio reps of a...

Mine are actually independent bio reps of a lab-grown plant, with different duration of application of a hormone ('duration' is a better word than 'time' in my case). So it's quite different from...
Forum: RNA Sequencing 02-04-2014, 04:13 PM
Replies: 8
Views: 7,552
Posted By samhokin
Ahhhh, thank you. That is really not very clear...

Ahhhh, thank you. That is really not very clear from the edgeR manual, or maybe I'm just too new to this approach to understand that. Seems subtle to me, but I am now enlightened!
Forum: RNA Sequencing 02-04-2014, 08:16 AM
Replies: 8
Views: 7,552
Posted By samhokin
Wait a sec. I'm looking at the edgeR User's...

Wait a sec. I'm looking at the edgeR User's Guide, section 3.3.1 "defining each treatment as a group", and I'm pretty much sure it says to do what I originally did. It says:

> lrt <- glmLRT(fit,...
Forum: RNA Sequencing 02-03-2014, 02:21 PM
Replies: 8
Views: 7,552
Posted By samhokin
Thanks, Dario! That tells me that my other...

Thanks, Dario! That tells me that my other "contrasts" aren't what I want, either. I don't want the difference between [the difference between Col30 and Col0] and [the difference between AS230 and...
Forum: RNA Sequencing 02-01-2014, 09:20 AM
Replies: 8
Views: 7,552
Posted By samhokin
coef vs contrast in edgeR glmLRT

I thought I understood what the contrast= option in glmLRT means as opposed to coef= (which just looks for DE wrt the index=1 sample, presumed to be the control), but I'm getting crazy results from...
Forum: Bioinformatics 12-27-2013, 07:49 AM
Replies: 18
Views: 9,919
Posted By samhokin
Thanks, celeste8!! :)

Thanks, celeste8!! :)
Forum: Site Feedback/Suggestions 12-21-2013, 06:15 AM
Replies: 7
Views: 16,351
Posted By samhokin
*BUMP* I'd really like tapatalk support. My...

*BUMP* I'd really like tapatalk support. My tablet browsers have trouble with the DHTML, like the search input.
Forum: RNA Sequencing 12-20-2013, 01:22 PM
Replies: 0
Views: 2,661
Posted By samhokin
Getting mapped read count from a BED file - bedtools coverage?

Hi, all. I've been trying to analyze an experiment that I downloaded from GEO, GSE34241, which has four samples assayed with RNA-Seq (AB SOLiD System). Apart from being interested in some gene...
Forum: Bioinformatics 11-10-2013, 07:42 AM
Replies: 16
Views: 3,371
Posted By samhokin
It also depends, of course, on which transcripts...

It also depends, of course, on which transcripts you're interested in. For example, if we were studying photosynthesis in Arabidopsis, 40M raw reads would be overkill, since the genes responsible for...
Forum: RNA Sequencing 11-10-2013, 07:28 AM
Replies: 1
Views: 1,405
Posted By samhokin
six huge read count outliers on neighboring transcripts on one lane - theories?

This is a purely academic question since these particular transcripts are not of particular interest to us (and they're only bad on one out of 71 lanes), but I'm curious as to what the theory may be...
Forum: Introductions 11-10-2013, 06:54 AM
Replies: 0
Views: 913
Posted By samhokin
Hello from Wisconsin

Hiya folks, I'm new to computational biology, got a gig doing analysis for Kathy Barton in the Department of Plant Biology at the Carnegie Institution for Science in Stanford, although I live in...
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