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Forum: De novo discovery 11-03-2014, 07:23 AM
Replies: 0
Views: 1,322
Posted By int11ap1
Question Finding repetitive elements from BAC sequences and Illumina sequences.

Hello to everybody,

I need to identify repetitive elements of 5 genotypes from the same species (a plant species that is not yet sequenced). For that, I have different datasets:

1) Illumina...
Forum: Metagenomics 10-06-2014, 09:52 AM
Replies: 1
Views: 1,375
Posted By int11ap1
Functional annotation

Hi everybody,

I am designing a novel pipeline for processing metagenomic datasets. I'd like to use for functional annotation the following methods:

1) Full domain alignment methods (e.g. Pfam...
Forum: RNA Sequencing 07-18-2014, 02:34 AM
Replies: 5
Views: 1,323
Posted By int11ap1
I do not understand how could I compare two...

I do not understand how could I compare two populations just doing a regression...

Another question, if I perform a Wilcoxon test for the other data and the two populations are significantly not...
Forum: RNA Sequencing 07-18-2014, 01:59 AM
Replies: 5
Views: 1,323
Posted By int11ap1
Because they are not normally distributed, right?...

Because they are not normally distributed, right? What if I apply a log transformation? They should be nearly normal then.

Could you be more specific about ordered logistic regression, please?
...
Forum: RNA Sequencing 07-18-2014, 01:24 AM
Replies: 5
Views: 1,323
Posted By int11ap1
Question Statistically validate number of exons and isoforms

Hello to everybody,

I was reading the following paper,



which has the following figure:

http://genome.cshlp.org/content/22/9/1775/F3.medium.gif
Forum: RNA Sequencing 07-17-2014, 11:52 AM
Replies: 12
Views: 4,677
Posted By int11ap1
But the arithmetic mean of my FPKM values will be...

But the arithmetic mean of my FPKM values will be normally distributed according to the central limit theorem. In large samples such as mine, t.test for skewed distributions should be fine:...
Forum: RNA Sequencing 07-17-2014, 11:36 AM
Replies: 12
Views: 4,677
Posted By int11ap1
Here you are, thanks¡ Why do not apply directly...

Here you are, thanks¡
Why do not apply directly the t-test¿ Where can I learn about it¿
Forum: RNA Sequencing 07-17-2014, 11:28 AM
Replies: 12
Views: 4,677
Posted By int11ap1
I do not follow you, sorry for asking again. ...

I do not follow you, sorry for asking again.

For example, I have 1000 FPKM values (from 1 RNA-seq sample) from 1000 transcripts. If I want to compare first 500 with second 500 transcripts (for...
Forum: RNA Sequencing 07-17-2014, 11:17 AM
Replies: 12
Views: 4,677
Posted By int11ap1
But those methods that you say (edgeR and DESeq)...

But those methods that you say (edgeR and DESeq) are for normalization between different samples or RNA-seq datasets...
Forum: RNA Sequencing 07-17-2014, 11:09 AM
Replies: 12
Views: 4,677
Posted By int11ap1
I do not need specific RNA-seq normalization here...

I do not need specific RNA-seq normalization here for what I want. Both sets of genes (actually I have transcripts) come from the same RNA-seq dataset (the same fasta). One dataset is made up of...
Forum: RNA Sequencing 07-15-2014, 12:12 AM
Replies: 12
Views: 4,677
Posted By int11ap1
t-test FPKM values

I have two sets of genes, and I'd like to have a boxplot and do a t-test in order to know if they have significantly different expressions or not.

However, my t-test p-value changes when using...
Forum: RNA Sequencing 04-24-2014, 06:46 AM
Replies: 0
Views: 933
Posted By int11ap1
Question Orthologous non-coding genes

Dear all,

I am doing an RNA-seq project, whose aim is to look for lncRNAs of different species. Once I have a set genes that give lncRNAs across different species, I would like to know which genes...
Forum: RNA Sequencing 04-15-2014, 10:41 PM
Replies: 1
Views: 1,031
Posted By int11ap1
Reads mapped to another chromosome in paired-end data of RNA-seq

Hello guys,

I am doing a project in RNA-seq data with some datasets that are paired-end data. After alignment with TopHat2, I have around 1-5% of reads whose mate is mapped to another chromosome....
Forum: RNA Sequencing 03-20-2014, 05:40 AM
Replies: 2
Views: 1,614
Posted By int11ap1
Thank you for the reply, TiborNagy. Nevertheless,...

Thank you for the reply, TiborNagy. Nevertheless, the packages you suggest work only with small RNA-seq data! What if my library is a cDNA library?

The aim is to find pre-miRNAs from my annotated...
Forum: RNA Sequencing 03-20-2014, 03:50 AM
Replies: 2
Views: 1,614
Posted By int11ap1
Question RNA-Seq: distinguish lncRNA of smRNA precursors

Hi everybody,

I have some data from RNA-seq. This data does NOT come from a library of small RNAs, but comes from a library of mRNAs and total RNA. From this data, I perform an alignment with...
Forum: Genomic Resequencing 01-17-2014, 06:58 AM
Replies: 1
Views: 2,038
Posted By int11ap1
SNP density

Hi guys,

This is my first thread here in this forum. I hope I'm writing this question into the correct category!

Well, I have called variants with samtools mpileup, where:

MAPQ=20 # min...
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