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Forum: Bioinformatics 05-29-2015, 02:29 PM
Replies: 3
Views: 3,297
Posted By jk1124
Thanks for your reply! I thought that if either...

Thanks for your reply! I thought that if either of the samples were to have more adapter contamination, it would be the first sample (with a high number of reads unmapped:too short). Is my thinking...
Forum: Bioinformatics 05-29-2015, 12:48 PM
Replies: 3
Views: 3,297
Posted By jk1124
STAR unmapped: too short

Hello,

I recently mapped 8 RNA-Seq samples using STAR. The samples are paired. The data in log.final.out for each sample look very similar to the sample's partner - with one exception.

I have...
Forum: Bioinformatics 03-23-2013, 12:00 PM
Replies: 3
Views: 1,549
Posted By jk1124
Let me rephrase my question more generally. What...

Let me rephrase my question more generally. What are the advantages and disadvantages of using a GLM over an exact test? I noticed, for example, that DESeq2 has defaulted to using GLMs for all...
Forum: Bioinformatics 03-20-2013, 07:57 PM
Replies: 3
Views: 1,549
Posted By jk1124
GLMs vs pairwise testing

I am looking for genes which are differentially expressed in any of 5 samples. Should I use a GLM or pairwise DE testing for this? I know that GLMs are included in DESeq and edgeR but am unsure how...
Forum: RNA Sequencing 12-06-2012, 06:52 AM
Replies: 4
Views: 2,828
Posted By jk1124
Thanks for your helpful response. I had looked...

Thanks for your helpful response. I had looked into DESeq, but it also didn't return what I expected (and also doesn't handle multi-mapping reads, which I have a lot of). I have been thinking our...
Forum: RNA Sequencing 12-01-2012, 09:06 AM
Replies: 4
Views: 2,828
Posted By jk1124
cuffdiff q values

I am having trouble understanding Cuffdiff q-values. I have a gene, for example, that appears to be differentially expressed but is not called so even when using either two or three replicates. In...
Forum: General 11-28-2012, 01:15 PM
Replies: 5
Views: 5,458
Posted By jk1124
I think this may be the answer, from the...

I think this may be the answer, from the Cufflinks homepage, regarding the 1.1.0 release:

"Some users have reported that Cufflinks or Cuffdiff crashes due to running out of memory when processing...
Forum: General 11-19-2012, 06:55 AM
Replies: 5
Views: 5,458
Posted By jk1124
I am also wondering this. Did you ever find an...

I am also wondering this. Did you ever find an answer?
Forum: General 11-15-2012, 11:16 AM
Replies: 3
Views: 1,266
Posted By jk1124
Great! Thanks for the advice.

Great! Thanks for the advice.
Forum: General 11-15-2012, 11:14 AM
Replies: 2
Views: 2,122
Posted By jk1124
Does this thread help?...

Does this thread help? http://seqanswers.com/forums/showthread.php?t=1835
Forum: RNA Sequencing 11-14-2012, 04:12 PM
Replies: 1
Views: 1,923
Posted By jk1124
Alternatively, might be a better idea to use a...

Alternatively, might be a better idea to use a count based method instead?
Forum: RNA Sequencing 11-14-2012, 10:36 AM
Replies: 1
Views: 1,923
Posted By jk1124
Comparing FPKM across samples

I have two RNA-Seq samples, one which I performed using Spike-In Controls and the other without Spike-Ins.

I mapped and assembled (Tophat, Cufflinks) the first using a reference assembly (-G...
Forum: RNA Sequencing 11-03-2012, 11:41 AM
Replies: 0
Views: 1,288
Posted By jk1124
quick tophat question: max # threads?

Does anyone know if there is a maximum number of threads you can run with tophat? I've read you can pretty much use all available processors, but I imagine at some point there's too much overhead for...
Forum: Bioinformatics 11-03-2012, 11:27 AM
Replies: 1
Views: 1,346
Posted By jk1124
this is probably unhelpful but really basic...

this is probably unhelpful but really basic questions to start:

are you unable to use the binaries available?

also, did you successfully install the boost and samtools packages first? I also...
Forum: General 11-02-2012, 01:33 PM
Replies: 3
Views: 1,266
Posted By jk1124
Decompressing a file - very basic question

Hi everyone,

I have been running my sequencing analysis on a remote server. The sequencing data that I receive is compressed (.gz), so what I upload onto the server is a compressed file. I have...
Forum: RNA Sequencing 10-25-2012, 01:43 PM
Replies: 0
Views: 1,106
Posted By jk1124
Cuffdiff: Importance Sampling and Variance Calculation

I have been reading about Cuffdiff, and this is what I understand of its variance calculation. It seems to fit a negative binomial distribution, calculating the variance across samples by using the...
Forum: RNA Sequencing 10-25-2012, 01:35 PM
Replies: 6
Views: 3,301
Posted By jk1124
I am also confused by the explanation for upper...

I am also confused by the explanation for upper quartile normalization provided by the Cufflinks page (i.e. adjusting for highly overexpressed genes), and would appreciate any insight on that, but...
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