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Search: Posts Made By: rodrigo.duarte88
Forum: Bioinformatics 05-19-2015, 08:17 AM
Replies: 11
Views: 10,330
Posted By rodrigo.duarte88
Although this is very obvious, it took me a...

Although this is very obvious, it took me a couple of days to realise that I couldn't simply create my own reference file from the genomic region of my interest (I was humbly downloading the sequence...
Forum: Bioinformatics 05-17-2015, 07:09 AM
Replies: 7
Views: 2,075
Posted By rodrigo.duarte88
I will try running option 1 since it's more...

I will try running option 1 since it's more correct, as far as I've been reading.

But anyway, you've been very helpful! Thanks so much!!
Forum: Bioinformatics 05-17-2015, 05:38 AM
Replies: 7
Views: 2,075
Posted By rodrigo.duarte88
Ah!! This is what I needed to know!! Yes, I am...

Ah!! This is what I needed to know!! Yes, I am trying to align my reads to a specific part of the chromosome due to computational limitations..

Thanks so much for your help!
Forum: Bioinformatics 05-17-2015, 03:25 AM
Replies: 7
Views: 2,075
Posted By rodrigo.duarte88
And yeah, I am aware the first column of the gtf...

And yeah, I am aware the first column of the gtf file needs to match the headers of my chr10.fa reference files (that I check with command "bowtie2-inspect --names chr10").. So i manually changed the...
Forum: Bioinformatics 05-17-2015, 03:19 AM
Replies: 7
Views: 2,075
Posted By rodrigo.duarte88
But, for example, say I downloaded the hg19...

But, for example, say I downloaded the hg19 version at the iGenomes page.. in the file I find the chr10.fa reference file, which I create the bowtie index (bt2 files).. then theres also a GTF file...
Forum: Bioinformatics 05-15-2015, 11:36 AM
Replies: 7
Views: 2,075
Posted By rodrigo.duarte88
bowtie index file & matching GTF for tophat2, for specific human genome cytoband

Are there examples of bowtie2 ref file (used for indexing with bowtie2-build) and the gtf file that matches that, so I can use them as standard for my mapping?

I am having trouble in creating the...
Forum: Bioinformatics 05-12-2015, 04:36 AM
Replies: 3
Views: 1,113
Posted By rodrigo.duarte88
I did use this option. I used all 8 cores of my...

I did use this option. I used all 8 cores of my PC, the machine (the cooling fan) sounded like a train for those 2 days. haha

Because our lab is interested in allele specific expression, we aimed...
Forum: Bioinformatics 05-12-2015, 04:04 AM
Replies: 0
Views: 872
Posted By rodrigo.duarte88
Allele specific expression in RNAseq - masked genome

Dear folks,

My lab is specialised in allele specific expression. We made allele specific expression measurement in a targetted polymorphism and found allele A 12% more expressed than allele T....
Forum: Bioinformatics 05-12-2015, 03:54 AM
Replies: 3
Views: 1,113
Posted By rodrigo.duarte88
mapping reads to single human chromosome

Dear colleagues,

I have started working with RNAseq very recently and got stuck with the following:

- Should I map my reads to the whole human genome or only to the chromosome I am interested?...
Forum: De novo discovery 05-12-2015, 03:46 AM
Replies: 0
Views: 1,550
Posted By rodrigo.duarte88
transcript discovery using paired end read Illumina

Dear folks,

I am quite new to RNAseq data analysis and would appreciate if anyone could guide me.

I am interested in simply finding out which transcripts of a single gene are expressed in a...
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