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Forum: Bioinformatics 03-09-2017, 07:08 PM
Replies: 0
Views: 1,795
Posted By pkstarstorm05
Advice on time-series RNA-seq analysis tool

Hi all,

I recently wrote a piece of software that performs a set of analyses and helps users visualize their time series RNA-seq data. I've been suggested to publish the software in a minor...
Forum: Bioinformatics 07-31-2016, 02:25 PM
Replies: 3
Views: 2,197
Posted By pkstarstorm05
Hi GenoMax and SylvainL, Thanks so much for...

Hi GenoMax and SylvainL,

Thanks so much for your suggestions and time! They were both very helpful.

For anyone later who comes across this post - I strongly urge you to familiarize yourself...
Forum: Bioinformatics 07-30-2016, 09:40 PM
Replies: 0
Views: 1,696
Posted By pkstarstorm05
Interpreting bizarre cross-correlation results

Hi all,

I'm working with an Estrogen Receptor Chip-seq data set and I'm using the SPP phantom peak quality tools to calculate cross correlation and the plots produced look very bizarre compared...
Forum: Bioinformatics 07-19-2016, 03:54 PM
Replies: 3
Views: 2,197
Posted By pkstarstorm05
Retrieving promoter sequences using gene symbol

Hi all,

I've been working on this for a few days and don't seem to be getting anywhere.

I have a list of gene symbols (example list below) that I need to use to retrieve promoter sequences for...
Forum: Bioinformatics 07-17-2016, 07:57 PM
Replies: 3
Views: 3,076
Posted By pkstarstorm05
This an old thread, but following up on that to...

This an old thread, but following up on that to anyone out there - if I do have uneven ChIP and input tags, what do I do about it? Is it necessary to do anything about this? Will it throw off...
Forum: RNA Sequencing 09-10-2015, 10:59 PM
Replies: 10
Views: 4,854
Posted By pkstarstorm05
Hi Brian - sorry I've got one more question...

Hi Brian -

sorry I've got one more question about bbmap's run information printing. Does bbmap produce an output log? There are stats printed out on the screen during a mapping run, but it looks...
Forum: RNA Sequencing 09-10-2015, 05:29 AM
Replies: 10
Views: 4,854
Posted By pkstarstorm05
Hey Brian - amaze balls advice and insight as...

Hey Brian - amaze balls advice and insight as always.

I was wondering if you had any suggestions for mouse annotation sources (ensemble, vs ucsc, etc) - or is that the same story as human...
Forum: Bioinformatics 02-19-2015, 07:44 PM
Replies: 2
Views: 1,020
Posted By pkstarstorm05
You most likely need to edit your directory paths...

You most likely need to edit your directory paths in the program files.

This is written in the README.TXT (as apposed to the lower case readme.txt lol)

2. Edit isoEMDir location in files under...
Forum: RNA Sequencing 01-14-2015, 10:38 PM
Replies: 3
Views: 4,351
Posted By pkstarstorm05
Reply-insert size calculation

Hi Brian ,

Sorry, I should have clarified that - I'm working on Mouse tissue.

So if I'm understanding this correctly - you're suggesting to run BBmap or BBmerge just to estimate the insert...
Forum: RNA Sequencing 01-14-2015, 08:56 PM
Replies: 3
Views: 4,351
Posted By pkstarstorm05
How to correctly estimate RNA-seq mean insert size and standard distribution

Hi SEQanswers community!

So I'm not sure if this has been posted - I poked around, but didn't find anything specific enough so I'll just ask:

I realize that specifying the mean insert size and...
Forum: Bioinformatics 09-03-2014, 12:27 AM
Replies: 2
Views: 3,056
Posted By pkstarstorm05
RNA-seq Exfold Tutorial

Hi everyone,

This is a beefy one... sort of.

I've set up a big RNA-seq experiment where I'm comparing pooled mouse samples. I've clipped off a bit of tissue and extracted the RNA, then for...
Forum: Bioinformatics 08-18-2014, 08:47 PM
Replies: 4
Views: 1,896
Posted By pkstarstorm05
Hi Brian - Immediately after submitting that...

Hi Brian -

Immediately after submitting that response, I went back and ran the usage for the program you suggested. This line in particular was useful:

java -ea -Xmx512m -cp <path>...
Forum: Bioinformatics 08-18-2014, 08:34 PM
Replies: 4
Views: 1,896
Posted By pkstarstorm05
Wow, thanks for the speedy response Brian. I...

Wow, thanks for the speedy response Brian.

I will admit that I'm a bit of a novice with bioinformatics. I'm working on my PhD in developmental and genetics - and despite being told that we...
Forum: Bioinformatics 08-18-2014, 06:53 AM
Replies: 4
Views: 1,896
Posted By pkstarstorm05
Smile Formatting a custom genome reference

Hi All,

I have a transgenic mouse whose genome I've sequenced and I'm interesting is answering a few questions concerning insertions, deletions, rearrangements, and transgene copy numbers, all of...
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