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Forum: Bioinformatics 03-14-2014, 12:38 PM
Replies: 6
Views: 2,435
Posted By nsl
Phew! Sindrle, I thought i had my work cut...

Phew!

Sindrle, I thought i had my work cut out. I couldn't make head or tail of things at first. Very kind of you. I am going through the manual and shall incorporate your advice in the process....
Forum: Bioinformatics 03-14-2014, 11:51 AM
Replies: 6
Views: 2,435
Posted By nsl
Thank you for the quick reply Sindrle. I am new...

Thank you for the quick reply Sindrle. I am new to this, may I bother you with a few more questions in the future if I get stuck?

sincerely,

nsl
Forum: Bioinformatics 03-14-2014, 11:20 AM
Replies: 6
Views: 2,435
Posted By nsl
Hi sindrle, Did you figure out how to input...

Hi sindrle,

Did you figure out how to input cuffdiff results into goseq?

Thanks
nsl
Forum: RNA Sequencing 08-05-2013, 10:55 PM
Replies: 2
Views: 1,366
Posted By nsl
Micheal, Thank you for being kind enough to...

Micheal,

Thank you for being kind enough to answer. I understand and agree. This field seems like a moving target and I wanted to know whether the protocol has changed.

I view and am shaping...
Forum: RNA Sequencing 08-04-2013, 07:02 PM
Replies: 2
Views: 1,366
Posted By nsl
Red face opinions on rna-seq validation

Hi,

I am close to writing up an article which we hope to submit for publication in the coming months. I have 4 rna seq treatments with 3 biological reps each. I've chosen a fairly small list of...
Forum: Bioinformatics 07-13-2013, 09:27 AM
Replies: 42
Views: 20,533
Posted By nsl
jp, I've been dealing with ngs data for a...

jp,

I've been dealing with ngs data for a short 3 yrs and not an expert. I started in 2010 with 1 replicate and after being exposed to the seqanswer and other bioinformatics communities realized...
Forum: Bioinformatics 07-12-2013, 09:12 AM
Replies: 42
Views: 20,533
Posted By nsl
jp, I'm afraid that is fact. no replication...

jp,

I'm afraid that is fact. no replication would not allow you a stand alone publication :(
Forum: Bioinformatics 07-08-2013, 06:57 AM
Replies: 42
Views: 20,533
Posted By nsl
Hi Charitra, I'm learning on the job like many...

Hi Charitra,
I'm learning on the job like many and am not an expert. :o
1. isn't a problem. I've experienced it too. But am not sure why that msg pops up.
2. Could it be that there is no FASTA...
Forum: Bioinformatics 07-04-2013, 06:18 AM
Replies: 42
Views: 20,533
Posted By nsl
If the gtf file is incompatible you will know, as...

If the gtf file is incompatible you will know, as your cufflinks output will show "0 FPKM" for every gene. As mentioned in the posts above, get it from igenomes just to be safe.

If cuffdiff went...
Forum: Bioinformatics 06-03-2013, 09:25 PM
Replies: 4
Views: 2,578
Posted By nsl
Thanks you both for the insight

Thanks you both for the insight
Forum: Bioinformatics 05-31-2013, 10:32 AM
Replies: 4
Views: 2,578
Posted By nsl
cuffdiff (v 2.1.1) p-values

I have rnaseq data which I analyzed using the latest versions of tophat-cufflinks-cuffdiff ( that includes the new dispersion methods)

The authors mention that, "Because the test is now based on...
Forum: RNA Sequencing 04-26-2013, 11:25 AM
Replies: 0
Views: 931
Posted By nsl
isoform , tss_group and splicing.diff outputs

I have data from 100bp SE sequencing for 4 conditions with 4 replicates/condition. I have a few questions . I used the tuxedo pipeline with the latest cuffdiff 2 ( with DEseq dispersion methods).
...
Forum: Bioinformatics 04-27-2012, 08:54 PM
Replies: 2
Views: 7,799
Posted By nsl
thank you :)

thank you :)
Forum: Bioinformatics 04-27-2012, 08:20 AM
Replies: 2
Views: 7,799
Posted By nsl
1 lane per treatment vs. multiplexing for rnaseq

Hi all,

I ran a pilot for an experiment which had 3 treatments using 1 lane per treatment . We have funds to pay for 3 more full lanes of sequencing. My question is

Should I run each treatment...
Forum: Bioinformatics 03-31-2012, 07:26 PM
Replies: 2
Views: 1,749
Posted By nsl
Not sure whether you fixed the problem, but I...

Not sure whether you fixed the problem, but I think you can you can use "Filter SAM" under "SAM TOOLs" in galaxy as an alternative.
Forum: Bioinformatics 07-19-2011, 11:58 AM
Replies: 42
Views: 20,533
Posted By nsl
sorry for the naive question, but does it matter...

sorry for the naive question, but does it matter whether the annotations are from UCSC or Ensemble? I used Ensemble and get "0" values as well.
Forum: Bioinformatics 07-19-2011, 11:47 AM
Replies: 3
Views: 2,570
Posted By nsl
Hi Mark, I find myself in your shoes, did...

Hi Mark,

I find myself in your shoes, did you figure out why you have FPKM of "0" for genes you know to be expressed? I also, find that if I use a reference annotation of dmel to run cufflinks I...
Forum: Bioinformatics 07-05-2011, 08:38 AM
Replies: 31
Views: 12,338
Posted By nsl
Hi Cole, I am using galaxy for my rna-seq...

Hi Cole,

I am using galaxy for my rna-seq analysis and am about to execute cuffdiff and am unsure about option -c. The default is a 1000 whereas the manual suggests 10. Could you please advice me?...
Forum: Bioinformatics 06-26-2011, 09:59 PM
Replies: 31
Views: 12,338
Posted By nsl
Hi Andrea (aeveland) and anyone who has insight, ...

Hi Andrea (aeveland) and anyone who has insight,

I have the same question about option -c in cuffdiff. Why are the defaults so different and how do they translate. If you found the answer would...
Forum: Bioinformatics 06-26-2011, 03:09 PM
Replies: 31
Views: 12,338
Posted By nsl
Hi Andrea (aeveland) and any one who has some...

Hi Andrea (aeveland) and any one who has some insight,

I have the same question about option -c in cuffdiff. Why are the defaults so different and how do they translate. If you found the answer...
Forum: Bioinformatics 06-20-2011, 07:41 AM
Replies: 0
Views: 1,337
Posted By nsl
Cufflinks/Cuffdiff...what next?

Hi,

I have RNA-seq samples that I have run cufflinks on. I am teaching myself to interpret the data. Can someone please let me know what I should do with the output. What is the next step?
...
Forum: RNA Sequencing 05-27-2011, 02:08 PM
Replies: 6
Views: 4,948
Posted By nsl
Dear chadn737, what length of reads...

Dear chadn737,




what length of reads and roughly what percentage were you referring to here?
also, how do you know you have to trim them?

thanks
Forum: RNA Sequencing 05-26-2011, 01:04 PM
Replies: 6
Views: 4,948
Posted By nsl
dear chadn737, Thank you for the pdf and the...

dear chadn737,

Thank you for the pdf and the explanation. I was told by the sequencing facility that they did not remove the adapters. I am puzzled b/c your explanation seems logical.
...
Forum: RNA Sequencing 05-26-2011, 12:21 PM
Replies: 6
Views: 4,948
Posted By nsl
dear chadn737, It is clear to me that now...

dear chadn737,

It is clear to me that now there is a "level zero" and I am at it ....sigh.

I used the the clip tool in Galaxy. I left all the settings pretty much on default except for...
Forum: Bioinformatics 05-26-2011, 11:58 AM
Replies: 29
Views: 29,453
Posted By nsl
Thank you.

Thank you.
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