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Forum: RNA Sequencing 01-12-2015, 05:16 AM
Replies: 4
Views: 4,322
Posted By seeker
Thanks for that. I was also sent this link which...

Thanks for that. I was also sent this link which explains why they do not provide this information.

https://support.bioconductor.org/p/57328/#57340
Forum: RNA Sequencing 01-07-2015, 02:08 PM
Replies: 4
Views: 4,322
Posted By seeker
No, I'm afraid I never figured it out. Perhaps...

No, I'm afraid I never figured it out. Perhaps this will spur others who might know how to share.
Forum: Bioinformatics 03-28-2014, 11:34 PM
Replies: 11
Views: 9,853
Posted By seeker
Good to know bw, thanks.

Good to know bw, thanks.
Forum: Bioinformatics 02-27-2014, 01:01 AM
Replies: 5
Views: 3,165
Posted By seeker
At the risk of hijacking my own thread. Does...

At the risk of hijacking my own thread. Does anyone know what's going on when the expression values are associated with more than one locus? eg. LOC100648144,LOC100648258 in the barplot? They are...
Forum: Bioinformatics 01-21-2014, 09:55 PM
Replies: 5
Views: 3,165
Posted By seeker
I searched and didn't see that. Thanks for...

I searched and didn't see that. Thanks for pointing me to it. Fingers crossed that the next version arrives fairly quickly.
Forum: Bioinformatics 01-20-2014, 09:52 PM
Replies: 5
Views: 3,165
Posted By seeker
Wow, really? Ugh. Thanks for that. Can you...

Wow, really? Ugh.

Thanks for that. Can you point me to where you found that info or if you found some other work around? I guess it's not the end of the world to rerun it but it is annoying.
Forum: Bioinformatics 01-20-2014, 04:43 AM
Replies: 5
Views: 3,165
Posted By seeker
Weird confidence intervals from Cuffdiff

Hi All,

Something odd seems to be going on with an analysis I'm doing. I have run the tuxedo suite through to using cummerbund but am seeing some genes which have confidence intervals that do not...
Forum: Bioinformatics 11-21-2013, 11:14 PM
Replies: 11
Views: 9,853
Posted By seeker
Hadn't seen those gff-tools. Will take a good...

Hadn't seen those gff-tools. Will take a good look for future reference. Turns out it was an issue with the long names in the fasta file and short names in the GFF3 file. A silly issue really!
Forum: Bioinformatics 11-21-2013, 07:49 AM
Replies: 11
Views: 9,853
Posted By seeker
I called it that in the post because it might be...

I called it that in the post because it might be unclear otherwise.

index created by first catenating all the .fa files then running:
#real name of the index
bowtie2-build Bter_gDNA.fa...
Forum: Bioinformatics 11-21-2013, 07:42 AM
Replies: 11
Views: 9,853
Posted By seeker
Thanks Geno, I'll take a look at that paper. I...

Thanks Geno, I'll take a look at that paper. I did build the genome index ahead of running tophat.

I have a hunch that it might be because sequence names are all filled with extra info. I'll try...
Forum: Bioinformatics 11-21-2013, 07:10 AM
Replies: 11
Views: 9,853
Posted By seeker
Tophat2 with GFF3 annotation fails to produce Bowtie index.

Hi all.

I'm trying to map paired end illumina reads to a reference genome with a GFF3 file for annotation info. I compiled the genome sequence from separate files of each linkage groups plus the...
Forum: RNA Sequencing 11-01-2012, 05:14 AM
Replies: 4
Views: 4,322
Posted By seeker
edgeR MDS plot: any way to get genes contributing to axes out?

Hi All,

I'm working with edgeR and have a MDS plot that is interesting but want to know which genes contribute to the two axes. Any suggestions of how to get this out?

Cheers!
Forum: Core Facilities 09-22-2011, 02:50 AM
Replies: 9
Views: 5,317
Posted By seeker
Ouch! This is the reason I'm looking to go...

Ouch! This is the reason I'm looking to go elsewhere, my core facility has taken as long! Although the files look ok. Sorry to hear about your experience. That's rough.
Forum: Core Facilities 09-22-2011, 02:44 AM
Replies: 9
Views: 5,317
Posted By seeker
Thanks for the input Marco. What exactly was the...

Thanks for the input Marco. What exactly was the issue (or issues) in your case? Some dept.mates have had good experiences with de novo genome sequencing and would like as much info as possible...
Forum: Core Facilities 09-22-2011, 02:24 AM
Replies: 9
Views: 5,317
Posted By seeker
what are people's experiences with BGI in terms...

what are people's experiences with BGI in terms of quality? In particular for RNAseq.
Forum: Bioinformatics 09-02-2011, 09:33 PM
Replies: 7
Views: 1,860
Posted By seeker
Oh, I was following the flow from here:...

Oh, I was following the flow from here: http://seqanswers.com/forums/showthread.php?t=7100&highlight=bfast+bwa

So, you make the fastq paired, then map using the same fastq file for the f3 and f5...
Forum: Bioinformatics 09-02-2011, 07:05 PM
Replies: 7
Views: 1,860
Posted By seeker
From the solid2fastq script that came with...

From the solid2fastq script that came with bfast+bwa. I made a seperate fastq for each of the F3 and F5 reads rather than paired.
Forum: Bioinformatics 09-02-2011, 04:17 PM
Replies: 7
Views: 1,860
Posted By seeker
Changed the name and still the same error. How...

Changed the name and still the same error. How could I ensure that all the names are in the same order?
Forum: Bioinformatics 09-02-2011, 10:02 AM
Replies: 7
Views: 1,860
Posted By seeker
The first and last 100 lines of reads are in the...

The first and last 100 lines of reads are in the same order. I've renamed the f5 files to bmf (which was a typo when making the files). Could that be responsible?
Forum: Bioinformatics 09-02-2011, 05:31 AM
Replies: 7
Views: 1,860
Posted By seeker
Assertion failed error in BFAST localalign

Hi all, I'm getting the following error when trying to combine bfast and bwa mapped reads. Any suggestions would be appreciated.

command:
bfast localalign -f rna.fasta -1 p1.f3.reads.bmf -2...
Forum: Bioinformatics 08-31-2011, 01:04 AM
Replies: 13
Views: 3,635
Posted By seeker
It looks like I was doing something stupid by...

It looks like I was doing something stupid by telling it to use more threads than made sense. Reducing that to the number of cores on my processor fixed the problem.
Forum: Bioinformatics 08-30-2011, 03:53 AM
Replies: 13
Views: 3,635
Posted By seeker
actually, it failed again with my real...

actually, it failed again with my real data..(above was with a small test file). any suggestions here would be great.
Forum: Bioinformatics 08-30-2011, 02:50 AM
Replies: 13
Views: 3,635
Posted By seeker
I am having a similar error running bfast match....

I am having a similar error running bfast match. It will go through one index (of 10 indexes) fine and then give the same malloc error followed by a message saying that it could not allocate enough...
Forum: Bioinformatics 08-17-2011, 05:38 AM
Replies: 7
Views: 3,473
Posted By seeker
any progress on this?

any progress on this?
Forum: RNA Sequencing 07-13-2011, 06:52 AM
Replies: 1
Views: 1,875
Posted By seeker
SOLiD RNAseq questions using galaxy and cuffdiff

hi all,

I'm a bit of a noob here. I'm working through some transcriptome data using galaxy and am having a couple troubles.

I have SOLiD data, paired end, but with the F5-BC tag. I have watched...
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