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Forum: Bioinformatics 03-11-2014, 07:30 AM
Replies: 2
Views: 2,140
Posted By jb2
You could also look into utilizing voom to...

You could also look into utilizing voom to transform the RSEM output for use in the limma package. Voom is found in the edgeR/limma R bioconductor packages.
Forum: Bioinformatics 02-07-2013, 09:16 AM
Replies: 13
Views: 2,903
Posted By jb2
TopHat allows reads to map to more than one place...

TopHat allows reads to map to more than one place in the genome (multihits). This can occur for reads that overlap with elements that repeat in the transcriptome. This means that those reads get...
Forum: Bioinformatics 01-23-2013, 09:28 AM
Replies: 2
Views: 1,098
Posted By jb2
I'm also interested in a potential answer to...

I'm also interested in a potential answer to this. I've merged a few gtf annotation files together using cuffcompare. These all have p_ids, and also lose the CDS data from the original gtf files....
Forum: Bioinformatics 01-17-2013, 11:07 AM
Replies: 6
Views: 4,976
Posted By jb2
I'm finding that over time all my jobs finish,...

I'm finding that over time all my jobs finish, but for some reason some get stuck here for much longer than other jobs, some running for five days with no movement before the thread finishes. I'm...
Forum: Bioinformatics 01-11-2013, 08:50 AM
Replies: 6
Views: 4,976
Posted By jb2
Also running into this issue with a lot of my...

Also running into this issue with a lot of my jobs getting stuck at 99% (using Cufflinks 2.0.2). Has anyone figured out this issue?
Forum: Bioinformatics 01-07-2013, 05:48 PM
Replies: 40
Views: 12,320
Posted By jb2
This is about the only way you could use a 1 vs....

This is about the only way you could use a 1 vs. 1 experiment in a way that would be legitimate. One other potential option is to rank your genes by fold change and use something like Gene Set...
Forum: Bioinformatics 01-07-2013, 02:58 PM
Replies: 8
Views: 1,815
Posted By jb2
For the most part they find evidence of...

For the most part they find evidence of expression for a large union of the splice junctions (both -G -T and -G --no-novel-juncs show that there are reads aligned to 175988 splice junctions).
...
Forum: Bioinformatics 01-07-2013, 02:23 PM
Replies: 8
Views: 1,815
Posted By jb2
Yep, both insertions.bed and deletions.bed are...

Yep, both insertions.bed and deletions.bed are there in both cases.

One thing I do notice, with -G --no-novel-juncs and -G -T, the resulting bam files do differ in size:

-G --no-novel-juncs

...
Forum: Bioinformatics 01-07-2013, 02:13 PM
Replies: 8
Views: 1,815
Posted By jb2
Oops, my bad! I just noticed that it does return...

Oops, my bad! I just noticed that it does return these things, just not in the place I originally checked. Doh! So now I'm going to go and explore what the difference might be between the...
Forum: Bioinformatics 01-07-2013, 02:03 PM
Replies: 8
Views: 1,815
Posted By jb2
Hi Amelie, Thanks for the response. What...

Hi Amelie,

Thanks for the response. What you stated does appear to be the case. I have also checked that the splice junctions in the junctions.bed file returned by tophat2 with -G and...
Forum: Bioinformatics 01-03-2013, 01:07 PM
Replies: 8
Views: 1,815
Posted By jb2
Tophat 2.0.4 -T and -G versus -G --no-novel-juncs

Hello everyone,

I've run into some ambiguity in the TopHat manual and was looking to see if anyone could help with my question.

I wanted to align my sequenced reads against the genome with a...
Forum: Bioinformatics 10-31-2012, 10:51 AM
Replies: 6
Views: 2,484
Posted By jb2
I'm also getting an issue with running cuffmerge...

I'm also getting an issue with running cuffmerge on >250 assemblies. The odd thing is that if I run with only a few assemblies, cuffmerge appears to work fine. It doesn't look like a memory issue...
Forum: Bioinformatics 05-05-2011, 01:57 PM
Replies: 31
Views: 11,623
Posted By jb2
Thumbs up Awesome!

This is great for many reasons. I think the new option to have Reference Annotation Based Transcript (RABT) assembly will be a really nice feature.

Furthermore, I'm excited to see how CuffDiff...
Forum: Bioinformatics 04-12-2011, 10:34 AM
Replies: 7
Views: 4,528
Posted By jb2
Just a note, it looks like the math for deriving...

Just a note, it looks like the math for deriving the significance is found on pages 26-28 of the Cufflinks paper supplemental pdf. It is still a bit bewildering, but maybe others can get a better...
Forum: Bioinformatics 04-11-2011, 01:10 PM
Replies: 7
Views: 4,528
Posted By jb2
I'm also very interested in getting information...

I'm also very interested in getting information as to how p-values are calculated from the square root of the Jensen–Shannon divergence. Based on my basic understanding, the larger the JS divergence,...
Forum: Bioinformatics 02-25-2011, 09:34 AM
Replies: 3
Views: 1,206
Posted By jb2
Yep, in order to handle this, I just wrote a...

Yep, in order to handle this, I just wrote a quick script to remove the read with the buggy CIGAR string and then ran samtools from there to create the bam files. You should be able to find the .sam...
Forum: Bioinformatics 01-25-2011, 09:49 AM
Replies: 5
Views: 6,219
Posted By jb2
Hi Lahoman, To my knowledge the -p argument...

Hi Lahoman,

To my knowledge the -p argument specifies the number of threads to use. This is based on using computers/clusters with multiple cores/processors. If you are running a dual core...
Forum: Bioinformatics 01-12-2011, 01:55 PM
Replies: 6
Views: 5,213
Posted By jb2
Thanks for your help on this. Is there a quick...

Thanks for your help on this. Is there a quick tool for removing lines with problematic cigar strings? I'm sure I could throw a script together in perl pretty quickly, otherwise, but just curious.
Forum: Bioinformatics 01-11-2011, 04:03 PM
Replies: 6
Views: 5,213
Posted By jb2
Tophat v1.1.4 potential error with sam to bam conversion?

Using tophat v1.1.4, I have run into some issues with running tophat on the Illumina Human Body Map data. Here is some information from the log files from the run.

---
Last few lines of output...
Forum: Bioinformatics 12-29-2010, 07:40 AM
Replies: 10
Views: 2,998
Posted By jb2
Thanks for the help from you and Cole!

Thanks for the help from you and Cole!
Forum: Bioinformatics 12-13-2010, 09:45 AM
Replies: 8
Views: 5,879
Posted By jb2
I am also getting similar error messages to...

I am also getting similar error messages to adumitri. The sqrt(det(cov)) issue was also mentioned in this thread: http://seqanswers.com/forums/showthread.php?t=6178
Forum: Bioinformatics 12-13-2010, 09:43 AM
Replies: 10
Views: 2,998
Posted By jb2
I haven't heard anything, but at least it is nice...

I haven't heard anything, but at least it is nice to know that I am not the only one seeing this error.
Forum: Bioinformatics 11-29-2010, 04:15 PM
Replies: 10
Views: 2,998
Posted By jb2
I am also getting the following error message and...

I am also getting the following error message and curious what exactly it means:

Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Forum: Bioinformatics 11-05-2010, 11:27 AM
Replies: 26
Views: 14,459
Posted By jb2
Yeah, that is what I was worried about, because I...

Yeah, that is what I was worried about, because I was considering taking those into account with my data. I will take a look at your script though since it saves me the time of writing my own.
...
Forum: Bioinformatics 11-04-2010, 03:24 PM
Replies: 26
Views: 14,459
Posted By jb2
I have also been getting some duplicates when...

I have also been getting some duplicates when examining the genes.expr file. Aligned using tophat to hg19 and used -G option in cufflinks 0.9.2 with ensembl 59 gtf file.

Any ideas?

See some...
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