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Forum: Bioinformatics 05-03-2018, 11:13 PM
Replies: 0
Views: 1,283
Posted By friducha
Tools to check consistency between VCF genotypes & pedigree-stated sex/relationship?

X-post from Biostars. (https://www.biostars.org/p/313118/)

We're currently trying to do identity checks on targeted genome sequencing data from ~15K samples. Our target panel is very specific, and...
Forum: Bioinformatics 07-17-2015, 10:46 AM
Replies: 2
Views: 2,155
Posted By friducha
Thanks, Michael. So it is clear to me now...

Thanks, Michael.

So it is clear to me now that the dispersion values are now per-gene, so gene-est-only no longer applies.

Quoting from the paper:




What about estimating the dispersions...
Forum: Bioinformatics 07-16-2015, 03:21 PM
Replies: 1
Views: 1,881
Posted By friducha
DESeq2 and GLM with grouped samples in two conditions

Hi all,

I came across this post (http://seqanswers.com/forums/showpost.php?p=72800&postcount=18) from Simon Anders, suggesting to use a GLM if one has grouped samples across the conditions.


...
Forum: Bioinformatics 07-16-2015, 03:03 PM
Replies: 2
Views: 2,155
Posted By friducha
What happened to per-condition and gene-est-only in DESeq2?

In DESeq, there was an option to estimate the gene dispersions within each condition instead of across all conditions, and per gene instead of sharing dispersion estimates across genes.

However,...
Forum: Bioinformatics 07-14-2015, 10:34 AM
Replies: 2
Views: 1,793
Posted By friducha
Hi, I am in a similar situation with my...

Hi,

I am in a similar situation with my data.

I have three conditions, with 4 replicates for CondA, 2 replicates for CondB, and 2 replicates for CondC.

When I run DESeq using all 8 samples,...
Forum: Bioinformatics 07-03-2015, 03:48 PM
Replies: 1
Views: 2,971
Posted By friducha
Start analysis from DESeq2-normalized read counts?

Hi all,

I know that DESeq2 relies on using raw read countsd as input. However, I have the following question:

What if the read counts were already normalized using DESeq2? Is there a way to...
Forum: Bioinformatics 07-03-2015, 03:16 PM
Replies: 5
Views: 3,704
Posted By friducha
Why sum technical replicates instead of averaging (and rounding) for DESeq?

It is widely recommended to sum technical replicate samples for differential gene expression analysis.
I was wondering why this is the case, and not averaging the technical replicates into a single...
Forum: Bioinformatics 02-26-2015, 02:56 PM
Replies: 15
Views: 10,951
Posted By friducha
I would also like to understand why using...

I would also like to understand why using spike-in controls for normalization is being discouraged here.
Forum: Bioinformatics 02-12-2015, 04:16 PM
Replies: 2
Views: 2,247
Posted By friducha
Must paired-end reads be in the same order in the two files for Tophat?

Hello,

Will TopHat work if R1.fastq and R2.fastq have their reads in different order?

What if R1.fastq has some reads whose R2 mate did not make it past QC, and viceversa (R2.fastq has some...
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