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Forum: Bioinformatics 04-23-2019, 02:07 PM
Replies: 0
Views: 479
Posted By JueFish
Maker AWS AMI

Anyone know where where I can find an already set up AWS AMI for running the Maker pipeline?

Thanks!
Forum: Bioinformatics 10-10-2013, 12:52 PM
Replies: 0
Views: 1,221
Posted By JueFish
unique kmers in genome equation?

Hi all,

Just trying to make sure I've got this right. Is this the correct equation for calculating the number of expected unique kmers in a library:

Number of expected unique kmer = genome size...
Forum: Bioinformatics 10-02-2013, 10:59 AM
Replies: 18
Views: 5,894
Posted By JueFish
Marie, Sorry for the long delay, but I lost...

Marie,

Sorry for the long delay, but I lost track of this thread. Yes, I did finish a bunch of this work, so if you still have any specific questions about what we did, please either add to this...
Forum: Bioinformatics 03-06-2013, 02:51 PM
Replies: 7
Views: 6,025
Posted By JueFish
RNA-seq and sense/antisense expression differences

Hello all,

Wondering if anyone out there could de-mystify the inner working of eXpress and edgeR for me or give me a better suggestion on how to do something. Basically, I'm looking at...
Forum: Bioinformatics 09-25-2012, 08:23 AM
Replies: 0
Views: 1,384
Posted By JueFish
Looking for positive selection pipeline suggestions

I need to set up some large scale assessments of lots of predicted transcripts from transcriptome assemblies for tests of positive selection. Does anyone have any specific suggestions on preferred...
Forum: RNA Sequencing 09-24-2012, 10:24 AM
Replies: 9
Views: 2,933
Posted By JueFish
ramma, 8MB is actually still smaller than what I...

ramma, 8MB is actually still smaller than what I need, but it's better than what I got. I can probably drop my reference down to get in that range. I'll send you a private message on Seqanswers and...
Forum: Bioinformatics 09-20-2012, 02:06 PM
Replies: 3
Views: 2,185
Posted By JueFish
Well, for future reference, if anyone runs into...

Well, for future reference, if anyone runs into this thread, I ended up using an on-line program called TagCleaner to identify possible primer tags in next-gen sequences and then cut them out using...
Forum: RNA Sequencing 09-20-2012, 02:03 PM
Replies: 9
Views: 2,933
Posted By JueFish
ramma, having similar issue using cufflinks on...

ramma, having similar issue using cufflinks on large transcriptome sequence with lots of predicted transcripts. How did you get the program to compile? When I change the hits.cpp file, it won't...
Forum: Bioinformatics 09-17-2012, 11:03 AM
Replies: 3
Views: 2,185
Posted By JueFish
Thanks for the response, bbeitzel. Yes, I...

Thanks for the response, bbeitzel. Yes, I noticed a common sequence as well, which is probably the Universal primer, in lots (~53% of all, ~5% at 3' end and ~48% at 5' end) of the reads, but not...
Forum: Bioinformatics 09-14-2012, 06:41 AM
Replies: 3
Views: 2,185
Posted By JueFish
Sigma Genomeplex Whole genome amplification primer removal

Someone recently asked me to help them build an assembly for some 454 data sequenced after using the Sigma/Aldrich Genomeplex Whole Genome Amplicification kit. Unfortunately, the primer sequencing...
Forum: Bioinformatics 08-08-2012, 01:13 PM
Replies: 10
Views: 9,376
Posted By JueFish
I have had some simliar issues with figuring out...

I have had some simliar issues with figuring out my fastx output. Has anyone spoken with the authors of the program? I haven't been able to glean much from their website or manual on the details...
Forum: Bioinformatics 04-26-2012, 11:23 AM
Replies: 0
Views: 1,069
Posted By JueFish
EST alignments without genome

Hi all,

Wondering if anyone could offer me some suggestions on how to approach an analysis. Currently, I am examining a transcriptome and looking at some "known" elements of that transcriptome...
Forum: SOLiD 04-18-2012, 08:48 PM
Replies: 4
Views: 2,221
Posted By JueFish
Thanks for the thoughts. We're definitely...

Thanks for the thoughts. We're definitely looking into the RiboZero kit as an alternative. What species have you guys used it on? Just human or other eukaryotes as well? We're wondering how well...
Forum: SOLiD 04-17-2012, 12:58 PM
Replies: 4
Views: 2,221
Posted By JueFish
Issues with SOLiD run

Hi all,

We finally got our SOLiD 5500 up and running and have run into a suite of problems we are currently trying to trouble-shoot. There are three specific issues which I will describe below,...
Forum: Bioinformatics 03-21-2012, 08:24 AM
Replies: 18
Views: 5,894
Posted By JueFish
Great discussion. We have noticed a similar...

Great discussion. We have noticed a similar issue with our first run of SOLiD 5500 data: poor mapping of ECC data vs. Lifescope; drop-off of quality metrics after first 20-25bp of reads, etc.. ...
Forum: Bioinformatics 02-22-2012, 09:54 AM
Replies: 5
Views: 12,544
Posted By JueFish
Lior only said they were trying to think of a...

Lior only said they were trying to think of a solution to this issue, but haven't come up with something satisfactory yet while trying to explore some possibilities using transcript coverage...
Forum: Bioinformatics 02-22-2012, 07:58 AM
Replies: 5
Views: 12,544
Posted By JueFish
Thanks for your thoughts, turnersd. I got an...

Thanks for your thoughts, turnersd. I got an email back from Cole Trapnell and Lior Pachter about this issue and it was pretty much as I thought. They seem to be trying to work on a bioinformatic...
Forum: Bioinformatics 02-11-2012, 10:40 PM
Replies: 5
Views: 12,544
Posted By JueFish
Significance of an FPKM value

Curious what some other people might be thinking about what I am seeing in the literature these days. Am I wrong that the general contention that people make that an FPKM value = 1 (estimated in...
Forum: Bioinformatics 11-11-2011, 03:02 PM
Replies: 19
Views: 9,070
Posted By JueFish
I really appreciate everyone's thoughts on this...

I really appreciate everyone's thoughts on this matter. Really interesting discussion. Brings up a couple more questions for me though.

1) In response to Rick's comments:

"Do the assembly...
Forum: Bioinformatics 11-10-2011, 08:00 AM
Replies: 19
Views: 9,070
Posted By JueFish
Color-space/SOLID assembly issues?

Hello all,

Our lab is about to undertake a large transcriptome sequencing project where we will be doing both de novo assembly of transcriptomes and RNA-seq comparisons across and within species...
Forum: Bioinformatics 08-24-2011, 08:52 AM
Replies: 0
Views: 1,329
Posted By JueFish
cufflinks, tophat, and mysterious snoRNAs

We have been looking at different tissue transcriptomes and noticed that when we estimate fpkm values (using RefSeq as an annotation) we get lots of snoRNAs as our most highly expressed entities (and...
Forum: Bioinformatics 08-24-2011, 08:00 AM
Replies: 9
Views: 8,281
Posted By JueFish
Well, camelbbs, "work" is an interesting way to...

Well, camelbbs, "work" is an interesting way to put it. I can let you in on what little I know, but I'm still trying to work through these things myself. Someone else out there might have some more...
Forum: Bioinformatics 08-24-2011, 07:56 AM
Replies: 9
Views: 8,281
Posted By JueFish
Well, camelbbs, "work" is an interesting way to...

Well, camelbbs, "work" is an interesting way to put it. I can let you in on what little I know, but I'm still trying to work through these things myself. Someone else out there might have some more...
Forum: Bioinformatics 08-23-2011, 02:34 PM
Replies: 9
Views: 8,281
Posted By JueFish
Hi camelbbs, Just saw your post and thought...

Hi camelbbs,

Just saw your post and thought I'd give you a word of caution. Make sure you take a look at your annotation closely. We just started to play around with the iGenomes stuff, but I'll...
Forum: Bioinformatics 08-23-2011, 02:28 PM
Replies: 9
Views: 8,281
Posted By JueFish
Hi camelbbs, Just saw your post and thought...

Hi camelbbs,

Just saw your post and thought I'd give you a word of caution. Make sure you take a look at your annotation closely. We just started to play around with the iGenomes stuff, but I'll...
Showing results 1 to 25 of 42

 


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