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Search: Posts Made By: adumitri
Forum: Bioinformatics 06-19-2015, 09:04 AM
Replies: 8
Views: 8,065
Posted By adumitri
Hi gr8guns, Did you figure out how to use...

Hi gr8guns,

Did you figure out how to use samtools to properly address your question? If so, it would be great if you could post your solution.
Forum: Bioinformatics 06-27-2013, 07:37 AM
Replies: 2
Views: 1,956
Posted By adumitri
Hi Alejandro, Thank you for your answer -...

Hi Alejandro,

Thank you for your answer - this is exactly what I was looking for!

Alexandra
Forum: Bioinformatics 06-21-2013, 04:00 PM
Replies: 2
Views: 1,956
Posted By adumitri
DEXSeq with experimental variables

Hi,

Can anyone let me know if the formulae displayed below are accurate when trying to account for two different experimental variables (batch and age) with DEXSeq? Also, what does the "I(exon ==...
Forum: Bioinformatics 05-03-2013, 01:34 PM
Replies: 1
Views: 2,411
Posted By adumitri
DESeq v1.12.0 estimateDispersions function: pooled-CR vs pooled

Hi,

I am using DESeq v1.12.0 to compare count data for ~6,000 exons in ~200 genes; these genes are the ones found to be significantly differentially expressed (FDR level) in a prior gene-centric...
Forum: Bioinformatics 04-05-2013, 06:52 PM
Replies: 4
Views: 6,416
Posted By adumitri
Hi chadn737, 1, 2) I will have to look into...

Hi chadn737,

1, 2) I will have to look into the DESeq2 R package - thanks for pointing this out.
3) In general, I would agree with you. Nevertheless, my question regarding the variance filters...
Forum: Bioinformatics 04-05-2013, 04:40 PM
Replies: 4
Views: 6,416
Posted By adumitri
RNA-Seq variance-based filter before differential expression analysis

Hello,

I am analyzing a larger set of RNA-Seq data (20 controls/20 diseased, Illumina Hi-Seq 2000, 101 bp, paired-end) in tissue that is affected in later stages of our disease of interest....
Forum: RNA Sequencing 01-17-2013, 07:15 AM
Replies: 5
Views: 4,483
Posted By adumitri
schelhorn, thank you for the references! They...

schelhorn, thank you for the references! They were very useful.
Forum: Bioinformatics 01-10-2013, 04:17 PM
Replies: 6
Views: 2,337
Posted By adumitri
Even if you do not use Cuffdiff for the DE...

Even if you do not use Cuffdiff for the DE analysis, you can run Cufflinks on your samples to get sample-specific .gtf files. These annotations (which can contain novel transcripts/genes) can be...
Forum: Introductions 01-03-2013, 02:40 PM
Replies: 0
Views: 1,267
Posted By adumitri
RNA-Seq optimal depth decision in human

Hi,

I was wondering if there are any new insights that anyone could share on the topic of RNA-Seq read depth. Assuming that the RNA samples are polyA-tail selected, and the sequencing is done with...
Forum: RNA Sequencing 01-03-2013, 02:25 PM
Replies: 5
Views: 4,483
Posted By adumitri
Hi malachig, I was wondering if there are...

Hi malachig,

I was wondering if there are any new insights that you could give me on the topic of RNA-Seq read depth. Assuming that the RNA samples are polyA-tail selected, and the sequencing is...
Forum: Bioinformatics 11-19-2012, 06:32 AM
Replies: 15
Views: 25,005
Posted By adumitri
Hi fpenagarican, Unfortunately, I did not...

Hi fpenagarican,

Unfortunately, I did not receive any relevant answer to my question. Still, I can confirm your results - with Cufflinks (and the corresponding Cuffdiff) v.2.0.0, there were no...
Forum: Bioinformatics 07-10-2012, 08:30 AM
Replies: 8
Views: 6,146
Posted By adumitri
Hi Simon, I do not fully understand your...

Hi Simon,

I do not fully understand your statement regarding RIN. Why did you say that RIN most likely does not influence expression in a linear fashion? Do you have any literature evidence that...
Forum: Bioinformatics 07-03-2012, 01:21 PM
Replies: 8
Views: 6,146
Posted By adumitri
Hi, I read Simon's answer from a few months...

Hi,

I read Simon's answer from a few months ago, but could not find details about covariates in the DESeq manual. The covariates I am interested in accounting for are quantitative and are known to...
Forum: Bioinformatics 06-19-2012, 02:28 PM
Replies: 15
Views: 25,005
Posted By adumitri
Hi, I was wondering if anyone had more...

Hi,

I was wondering if anyone had more thoughts about dejavu2010's comment... It is still not clear to me if Cuffdiff is built to analyze differential expression for groups of biological...
Forum: RNA Sequencing 05-22-2012, 08:34 AM
Replies: 3
Views: 3,132
Posted By adumitri
Hi craigb, Thank you for your post - it was...

Hi craigb,

Thank you for your post - it was useful. I was wondering if you found out anything else about the warning message you mentioned:

Warning: malformed line 1, missing columns
track...
Forum: RNA Sequencing 05-17-2012, 02:51 PM
Replies: 0
Views: 1,633
Posted By adumitri
Question about Cufflinks Log Output

Hi,

I was wondering if anyone could help me interpret the following part of Cufflinks' output:

> Map Properties:
> Normalized Map Mass: 284238.81
> Raw Map Mass: 284238.81
> ...
Forum: Bioinformatics 05-17-2012, 02:29 PM
Replies: 12
Views: 3,215
Posted By adumitri
This was very useful! Thank you again.

This was very useful! Thank you again.
Forum: Bioinformatics 05-17-2012, 02:22 PM
Replies: 12
Views: 3,215
Posted By adumitri
Hi cedance, did you mean splitting (instead of...

Hi cedance, did you mean splitting (instead of merging) the biological replicates in your post? Is there a standard way of doing this, or did you have to write your own script to get the replicates...
Forum: Bioinformatics 05-17-2012, 09:58 AM
Replies: 12
Views: 3,215
Posted By adumitri
Thank you, cedance! The number of sequences for...

Thank you, cedance! The number of sequences for each of our samples is at least 25 million, so I will start mapping each sample individually as a first step. I might go back to mapping all samples...
Forum: Bioinformatics 05-17-2012, 09:03 AM
Replies: 12
Views: 3,215
Posted By adumitri
TopHat2 run on individual or multiple samples

Hello,

I am trying to decide what the best approach for running TopHat2 is. We have multiple RNA-Seq samples for two different conditions. Is it preferable to run TopHat2 for each individual...
Forum: Bioinformatics 04-23-2011, 08:12 PM
Replies: 4
Views: 3,748
Posted By adumitri
Hi, Hopefully, this is the right place to...

Hi,

Hopefully, this is the right place to post my question:

I ran TopHat v1.2.0 on single reads (40 ntds) generated with Illumina GA IIx. These were the used options:

tophat --max-multihits...
Forum: Bioinformatics 12-13-2010, 09:06 AM
Replies: 8
Views: 6,474
Posted By adumitri
Hi, It does not seem like anyone had solved...

Hi,

It does not seem like anyone had solved the problem mentioned in this thread, but I am hoping that someone could help me with a similar problem. I am using the latest version of Cufflinks...
Forum: Bioinformatics 12-08-2010, 12:02 PM
Replies: 4
Views: 2,513
Posted By adumitri
Tophat v1.1.4 bug - cannot handle non-numeric versions of Samtools

Hi,

I was just using the new version of Tophat with Samtools-0.1.12a and got the following error:

[Wed Dec 8 16:56:42 2010] Beginning TopHat run (v1.1.4)...
Forum: Bioinformatics 12-07-2010, 08:40 AM
Replies: 38
Views: 21,677
Posted By adumitri
Thank you both for your help! It would be...

Thank you both for your help!

It would be great if anyone from the Cuffdiff team would be able to comment on how exactly the program decides on differential expression between groups. I am not...
Forum: Bioinformatics 12-07-2010, 07:54 AM
Replies: 38
Views: 21,677
Posted By adumitri
Hi Thomas, Can you be more specific? ...

Hi Thomas,

Can you be more specific?

From the Cuffdiff manual I understand that technical replicates are supported, but not biological replicates. For example, if I have 3 control and 4...
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