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Forum: Bioinformatics 04-08-2013, 07:49 AM
Replies: 0
Views: 2,291
Posted By griffon42
RNA-Seq analysis: Paired design with mutliple time points

Hi all,

I've got a relatively complex RNA-Seq experiment and I was hoping to get some input on analysis options. I've dug around quite extensively in these forums and others, but haven't been able...
Forum: RNA Sequencing 03-26-2013, 01:54 PM
Replies: 0
Views: 1,713
Posted By griffon42
Tophat and/or Cufflinks: strict splice donor/acceptor requirements?

Hello all --

I have a question regarding Tophat's handling of sequence data at splice donor/acceptor junctions:

When calling a splice junction/splitting a read across an intron, does Tophat...
Forum: Bioinformatics 03-07-2013, 12:46 PM
Replies: 313
Views: 124,310
Posted By griffon42
I've recently installed SeqMonk - it really looks...

I've recently installed SeqMonk - it really looks great, and should be very useful for some of the analyses I'm interested in running. Many thanks to the developers!

However, I've run into a...
Forum: Bioinformatics 01-03-2013, 03:00 PM
Replies: 6
Views: 4,796
Posted By griffon42
Any progress?

Has anyone figured this out? I'm struggling as well. In ggplot2, it seems like the issue is an inability to change the "default" layer of the plot, on account of the "data" being fed from the method,...
Forum: Bioinformatics 07-14-2010, 02:49 PM
Replies: 5
Views: 5,731
Posted By griffon42
I'm experiencing the same issue. I'm using...

I'm experiencing the same issue. I'm using cufflinks 0.8.3 (the 7/2 release) and the -c option doesn't seem to work as described in the manual. As extreme examples, I have loci that are "OK" for...
Forum: Bioinformatics 07-13-2010, 08:04 AM
Replies: 10
Views: 3,478
Posted By griffon42
Still really looking for some assistance on this...

Still really looking for some assistance on this - I'm totally stumped. Anyone have any ideas?

Thanks.
Forum: Bioinformatics 07-02-2010, 08:10 AM
Replies: 10
Views: 3,478
Posted By griffon42
Cuffcompare Xlocus error

Hi all -

I've been struggling with a strange error in CuffCompare.

I'm using the new cufflinks package (0.8.3) for 4 samples mapped using Tophat. After generating Cufflinks GTFs for each...
Forum: Bioinformatics 12-29-2009, 08:48 PM
Replies: 34
Views: 18,254
Posted By griffon42
Cufflinks outputs duplicate GTF entries?

Hi all-

First off, thank you Cole for Cufflinks. It will be very useful for the type of RPKM analysis I'd like to.

I'm having a bit of trouble with the GTF output files when I plug them into...
Forum: Illumina/Solexa 08-24-2009, 04:41 PM
Replies: 18
Views: 6,982
Posted By griffon42
Though I also think PCR bias is likely the...

Though I also think PCR bias is likely the primary culprit here, you might also consider problems caused during read mapping. Depending on which mapping/alignment algorithm you are using (and the...
Forum: Bioinformatics 08-05-2009, 06:10 PM
Replies: 6
Views: 2,956
Posted By griffon42
Tophat does a really nice job mapping splice...

Tophat does a really nice job mapping splice junctions without a set of known splice sites. It works very well with short Solexa reads, though I presume it requires a certain degree of read depth.
Forum: Bioinformatics 08-04-2009, 03:36 PM
Replies: 22
Views: 9,740
Posted By griffon42
Great! Looking forward to the update. I can...

Great! Looking forward to the update.

I can still email you sample data if necessary...just let me know.

Thanks again.
Forum: Bioinformatics 08-04-2009, 03:01 PM
Replies: 22
Views: 9,740
Posted By griffon42
Thanks Cole. Sorry for the sequential...

Thanks Cole.

Sorry for the sequential posting, but...Taking a closer look, it looks like the issue could be the base qualities returned in the 'accepted_hits.sam' output from Tophat.

I'm using...
Forum: Bioinformatics 08-04-2009, 02:28 PM
Replies: 22
Views: 9,740
Posted By griffon42
Is there any way to have Tophat output an...

Is there any way to have Tophat output an appropriate value for the "Mapping Qualities" field in the SAM format? At present, it outputs a straight "255" (which the SAM specification suggests when...
Forum: Bioinformatics 08-04-2009, 09:39 AM
Replies: 292
Views: 172,196
Posted By griffon42
To add a bit to xguo's questions regarding the...

To add a bit to xguo's questions regarding the varFilter in samtools:

I'm also struggling to understand the differences in varFilter relative to MAQ's SNPfilter. Using the exact same set of...
Forum: Bioinformatics 08-03-2009, 08:21 AM
Replies: 22
Views: 9,740
Posted By griffon42
Tophat 1.0.10

Hi Cole-

The new version (1.0.10) seems to be working fine for me. Strand orientation in the output SAM file looks good, as far as I can tell.

Thanks so much for the rapid turnaround!
Forum: Bioinformatics 07-30-2009, 05:28 PM
Replies: 3
Views: 5,807
Posted By griffon42
Thanks. That makes things considerably more...

Thanks. That makes things considerably more clear.
Forum: Bioinformatics 07-30-2009, 05:27 PM
Replies: 22
Views: 9,740
Posted By griffon42
Read orientation in Tophat SAM output

Though I've been successful in getting Tophat's SAM output into a SAMtools pileup, I've been having considerable trouble with a related issue.

According to the SAM specifications, for each...
Forum: Bioinformatics 07-23-2009, 07:42 AM
Replies: 3
Views: 5,807
Posted By griffon42
Interpretation of columns in MAQ SNP output?

Hi all-

Apologies if this information has been posted elsewhere - I wasn't able to find what I was looking for searching the forums.

I'm using MAQ cns2SNP (and SNPfilter) to call SNPs on short...
Forum: RNA Sequencing 04-30-2009, 12:11 PM
Replies: 25
Views: 14,032
Posted By griffon42
Hey Ali- Just wanted to say thanks for your...

Hey Ali-

Just wanted to say thanks for your help. Reducing the cache size seemed to help get through the analysis without memory errors, despite taking a bit longer.

I've got some additional...
Forum: RNA Sequencing 04-24-2009, 11:28 AM
Replies: 25
Views: 14,032
Posted By griffon42
Thanks Ali - I'm running ERANGE locally on a...

Thanks Ali -

I'm running ERANGE locally on a MacBook Pro with 4gb RAM, and not running ANYTHING else during the analysis. I've got the cache set to 2000000 for the RDS file.

This has been more...
Forum: RNA Sequencing 04-24-2009, 09:24 AM
Replies: 25
Views: 14,032
Posted By griffon42
ERANGE error message

Hi all-

I've used successfully used ERANGE3.0.1 in the past for some RNA-seq analysis. I'm now running into some problems getting through the RunStandardAnalysis script.

My reads are...
Forum: RNA Sequencing 02-20-2009, 03:49 PM
Replies: 25
Views: 14,032
Posted By griffon42
Also struggling with ERANGE...

Not sure if this thread is still going, but i'll give it a shot.

I'm also trying to get ERANGE (v2.1) off the ground and having some major problems.

I'm running through the shell on Mac OS X...
Forum: Bioinformatics 02-20-2009, 07:51 AM
Replies: 99
Views: 47,747
Posted By griffon42
Mapview overflow error

@baohua100

Thanks for all of your work on MapView...it's been very helpful so far and for the most part, working well.

I am having one problem that's given me some trouble. I'm using MapView...
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