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Search: Posts Made By: diego diaz
Forum: Bioinformatics 11-23-2015, 12:00 PM
Replies: 0
Views: 1,418
Posted By diego diaz
SNPeff annotations

Hi all,

I have a little doubt about the SNPeff annotations:

Reading some documentation, I found the list of the Sequence Ontology Terms used to annotate the variants. There are 45 Terms, which...
Forum: Bioinformatics 08-14-2015, 08:17 AM
Replies: 0
Views: 1,388
Posted By diego diaz
vcf-merge problem

Hi all

I am trying to merge several vcf files coming from the same genome. I am using vcftools, but the problem is that i am getting an empty output file:(.

First, I compressed all my sorted...
Forum: Bioinformatics 07-20-2015, 01:58 PM
Replies: 1
Views: 1,092
Posted By diego diaz
I forgot to mention that the variants were called...

I forgot to mention that the variants were called in the scaffolds not in the chromosomes, then I had to code a custom script to transform scaffolds coordinates into chromosomes coordinates, maybe...
Forum: Bioinformatics 07-20-2015, 01:53 PM
Replies: 1
Views: 1,092
Posted By diego diaz
Question strange behavior in vcftools

Hi all,

I want to split my VCF file into two files, one with SNPs and another with INDELs. To that I am using VCF tools, with the following sentences:

# to keep only SNPs
vcftools --vcf...
Forum: Bioinformatics 05-04-2015, 09:16 AM
Replies: 4
Views: 1,197
Posted By diego diaz
About the second question, what do you think is...

About the second question, what do you think is the best approximation to perform the analysis? smallRNA-seq or total RNA-seq?
Forum: Bioinformatics 05-04-2015, 08:27 AM
Replies: 4
Views: 1,197
Posted By diego diaz
Thanks GenoMax !

Thanks GenoMax !
Forum: Bioinformatics 05-04-2015, 07:07 AM
Replies: 4
Views: 1,197
Posted By diego diaz
Other question. My bosses said to me that in...

Other question. My bosses said to me that in literature has been reported that the exosomes can contain some mRNA molecules. To exosome profiling is more suitable using total RNA-seq (smallRNA +...
Forum: Bioinformatics 05-04-2015, 06:46 AM
Replies: 4
Views: 1,197
Posted By diego diaz
Coverage dept needed for Exosomes

Hi all,

In my lab, we want to characterize (only characterize, not differential expression) RNA elements inside of exosomes, by using sequencing. My bosses want to make a pool of several samples....
Forum: Bioinformatics 05-04-2015, 06:35 AM
Replies: 3
Views: 1,590
Posted By diego diaz
Hi, There are two ways to purify your...

Hi,

There are two ways to purify your RNA-seq data, Ribo-Zero and Poly(A). The first one only filters out the ribosomal RNA, keeping coding and small non coding RNA. Focused on valuable RNA...
Forum: Bioinformatics 04-30-2015, 04:57 AM
Replies: 5
Views: 1,545
Posted By diego diaz
Thanks GenoMax and Richard for your help !

Thanks GenoMax and Richard for your help !
Forum: Bioinformatics 04-29-2015, 01:37 PM
Replies: 5
Views: 1,545
Posted By diego diaz
I was trying with Mus musculus mm9 :)

I was trying with Mus musculus mm9 :)
Forum: Bioinformatics 04-29-2015, 11:30 AM
Replies: 5
Views: 1,545
Posted By diego diaz
How to retrieve EST data from UCSC

Hi all

I have some genomic coordinates, in BED format, that I want to check with ESTs. I tried to download EST data from UCSC, in bed format, but I couldn't. In the table browser, I selected "mRNA...
Forum: Bioinformatics 04-23-2015, 07:49 AM
Replies: 14
Views: 9,043
Posted By diego diaz
Yes, one has to be very careful to analyze this...

Yes, one has to be very careful to analyze this sort of experiments. As you said, from the extraction until the differential expression analysis, there are a lot of sources of bias, PCR...
Forum: Bioinformatics 04-23-2015, 06:42 AM
Replies: 14
Views: 9,043
Posted By diego diaz
Deseq2 also has good functions to normalize the...

Deseq2 also has good functions to normalize the count data, rlog transformation and varianceStabilizingTransformation. But be careful, they said in their tutorial

"The variance stabilizing and...
Forum: Bioinformatics 04-23-2015, 06:27 AM
Replies: 1
Views: 1,018
Posted By diego diaz
to get all the reads mapped in proper pair : ...

to get all the reads mapped in proper pair :

samtools view -F 3 yourbam.bam > properlypaired.bam

to get all the reads mapped in not proper pair :

samtools view -f 3 yourbam.bam >...
Forum: Bioinformatics 04-23-2015, 05:59 AM
Replies: 14
Views: 9,043
Posted By diego diaz
This is a good tutorial to perform differential...

This is a good tutorial to perform differential expression analysis

http://www-huber.embl.de/pub/pdf/nprot.2013.099.pdf

Here, they use htseq-count to count the number of reads per gene, and...
Forum: Bioinformatics 04-22-2015, 06:47 PM
Replies: 5
Views: 26,699
Posted By diego diaz
Yes, sorry, my mistake. The offset is added to...

Yes, sorry, my mistake. The offset is added to the counts, not to the cpm.
Forum: Bioinformatics 04-22-2015, 06:54 AM
Replies: 5
Views: 26,699
Posted By diego diaz
To calculate CPM manually in R it would be : ...

To calculate CPM manually in R it would be :

cpm <- apply(countmatrix,2, function(x) (x/sum(x))*1000000)

# the 1 added to log function is to avoid log 0 values
log.cpm <- log(cpm + 1)

To...
Forum: Bioinformatics 04-22-2015, 06:16 AM
Replies: 6
Views: 1,881
Posted By diego diaz
This is a good tutorial to perform differential...

This is a good tutorial to perform differential expression analysis with Deseq2

http://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data/

Most popular programs to perform...
Forum: Bioinformatics 04-22-2015, 06:07 AM
Replies: 14
Views: 9,043
Posted By diego diaz
Ok, I didn't know, thanks for the information :D ...

Ok, I didn't know, thanks for the information :D

Genomax is right, you have to be sure that your reference and your gtf have the same version. For example, is you map your reads to the genome...
Forum: Bioinformatics 04-21-2015, 06:40 AM
Replies: 8
Views: 2,352
Posted By diego diaz
If the genome is annotated then it is probably...

If the genome is annotated then it is probably that it is available in UCSC or Ensembl. In these repositories you could get a lot of curated genomic features, such us, repeat regions, TSSs, coding...
Forum: Bioinformatics 04-21-2015, 06:09 AM
Replies: 8
Views: 2,352
Posted By diego diaz
but what do you have to do? maybe there is an...

but what do you have to do? maybe there is an easier way to do it, instead using IGV

Do you have to analyze an unannotated genome?
Forum: Bioinformatics 04-21-2015, 05:36 AM
Replies: 8
Views: 2,352
Posted By diego diaz
Be careful with that GFF, it is weird to have a...

Be careful with that GFF, it is weird to have a promoter region with a 1 base long (1100 - 1101)
Forum: Bioinformatics 04-17-2015, 11:34 AM
Replies: 14
Views: 9,043
Posted By diego diaz
Red face "In my case, there are no attributes to choose...

"In my case, there are no attributes to choose from at all. So doesn't it seem kind of silly to add one?"

You have only one attribute, tandem_repeat, in the third column. But anyway you have to...
Forum: Bioinformatics 04-17-2015, 08:22 AM
Replies: 14
Views: 9,043
Posted By diego diaz
Hi Elizabeth The attribute line is necessary...

Hi Elizabeth

The attribute line is necessary because a GTF can have several attributes, for example, when you are counting the number of reads per gene, your GTF file will have gene entries, exon...
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