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Search: Posts Made By: rebrendi
Forum: Bioinformatics 05-06-2013, 09:47 AM
Replies: 5
Views: 8,642
Posted By rebrendi
Simon, I completely agree with the arguments,...

Simon, I completely agree with the arguments, just want to make sure things did not change during these two years: is it still common NOT to normalize by input?
Forum: Bioinformatics 03-21-2013, 11:30 AM
Replies: 1
Views: 2,009
Posted By rebrendi
Question GEM .map file format?

Hello,

I am analyzing the data for which the author has said that the data have been mapped with GEM. The file names have the extension .map. The content of the first lines is pasted below. Is it...
Forum: Bioinformatics 09-02-2012, 04:27 AM
Replies: 11
Views: 2,799
Posted By rebrendi
so these were all-zero in all 134 replicates, or...

so these were all-zero in all 134 replicates, or just in some fraction of them?
Forum: Bioinformatics 09-02-2012, 04:26 AM
Replies: 11
Views: 2,799
Posted By rebrendi
Thank you, great article!

Thank you, great article!
Forum: Bioinformatics 09-01-2012, 02:25 PM
Replies: 11
Views: 2,799
Posted By rebrendi
I am using Eldorado, it contains much more than...

I am using Eldorado, it contains much more than RefSeq, so more noise. But I am getting non-zero expression for these 9% transcripts in one cell line, and zero expression in another line, so this is...
Forum: Bioinformatics 09-01-2012, 01:51 PM
Replies: 11
Views: 2,799
Posted By rebrendi
Yes, that would be the best check. I have...

Yes, that would be the best check. I have actually, for one of the cell lines, two replicate experiments with 30,000 and 5,000 mapped reads. Both of them have these ~8-9% transcripts with zero reads.
Forum: Bioinformatics 09-01-2012, 01:36 PM
Replies: 11
Views: 2,799
Posted By rebrendi
and you considered that all those transcripts...

and you considered that all those transcripts have no expression, or just the signal is missing?
Forum: Bioinformatics 09-01-2012, 12:33 PM
Replies: 11
Views: 2,799
Posted By rebrendi
RNA-seq results interpretation - help needed

Hello,

I am using a standard procedure for RNA-seq, then TopHat followed by DeSeq to determine differential expression in my cell lines from the total RNA sequencing. I am using 2-3 replicates per...
Forum: Bioinformatics 06-05-2012, 04:54 AM
Replies: 6
Views: 2,106
Posted By rebrendi
I have the same error. Any ideas what's the...

I have the same error. Any ideas what's the problem?
Forum: Bioinformatics 03-27-2012, 01:27 PM
Replies: 1
Views: 1,792
Posted By rebrendi
Let's simplify the question a bit. There are WIG...

Let's simplify the question a bit. There are WIG files from ENCODE available at the UCSC Genome Browser, but there are no BED files. I also did not find BED files with TF enrichments from ENCODE in...
Forum: Bioinformatics 03-27-2012, 03:02 AM
Replies: 1
Views: 1,792
Posted By rebrendi
How to get TF binding sites from the ENCODE data?

Hello,

I am trying to extract the coordinates of TF binding sites from the ENCODE data, but have now realized that they only report broad peaks (~1000 bp) and not the exact binding sites. Is there...
Forum: Bioinformatics 03-27-2012, 02:23 AM
Replies: 10
Views: 7,695
Posted By rebrendi
you are right, have to contact the authors...

you are right, have to contact the authors...
Forum: Bioinformatics 03-27-2012, 01:56 AM
Replies: 13
Views: 2,759
Posted By rebrendi
are the summits exactly in the middle between the...

are the summits exactly in the middle between the peak start/end?
Forum: Bioinformatics 03-27-2012, 01:52 AM
Replies: 10
Views: 7,695
Posted By rebrendi
nope. it is provided as is by the authors

nope. it is provided as is by the authors
Forum: Bioinformatics 03-26-2012, 01:17 PM
Replies: 13
Views: 2,759
Posted By rebrendi
How to get TF binding sites from ChIP-Seq

Hello all,

I have the following question: suppose I have a ChIP-Seq data for a protein enrichment, and I made peak calling, e.g. with MACS, and obtained, say, 40,000 peaks with a width around...
Forum: Bioinformatics 03-26-2012, 01:04 PM
Replies: 10
Views: 7,695
Posted By rebrendi
dpryan, I am not looking for motifs, just need...

dpryan, I am not looking for motifs, just need the coordinates for each TF binding site (assuming that each peak contains one binding site). There is no single consensus motif for this TF, that is...
Forum: Bioinformatics 03-26-2012, 01:00 PM
Replies: 11
Views: 8,520
Posted By rebrendi
looks like a custom script is needed

looks like a custom script is needed
Forum: Bioinformatics 03-26-2012, 12:52 PM
Replies: 10
Views: 7,695
Posted By rebrendi
dpryan, thank you. concerning my second...

dpryan, thank you.

concerning my second question: is it safe to assume that the TF binding site is located in the middle of the identified broad peak (start+end)/2 ?
Forum: Bioinformatics 03-25-2012, 05:15 AM
Replies: 10
Views: 7,695
Posted By rebrendi
MACS output format (NAME_peaks.bed)

Hi all,

I am analyzing a ChIP-Seq output file with TF enrichment peaks from the published dataset. It looks like the data are in the MACS output format. The files are named "NAME_peaks.bed" and...
Forum: Bioinformatics 03-25-2012, 05:03 AM
Replies: 1
Views: 2,295
Posted By rebrendi
is it really the score in the last column of the...

is it really the score in the last column of the "NAME_peaks.bed" file?
Forum: Bioinformatics 03-03-2012, 05:28 PM
Replies: 31
Views: 4,828
Posted By rebrendi
I have found another TSS database:...

I have found another TSS database: http://dbtss.hgc.jp/index.html
Again, the coordinates do not coincide for several manually checked genes.
Is it really that difficult to determine TSS...
Forum: Bioinformatics 03-03-2012, 01:00 PM
Replies: 31
Views: 4,828
Posted By rebrendi
I am not that good in this particular topic, and...

I am not that good in this particular topic, and it is not a question of minutes anyway. It took me several weeks just to realize (by chance!) that something was going wrong with Yeast.

Now, with...
Forum: Bioinformatics 03-03-2012, 09:37 AM
Replies: 31
Views: 4,828
Posted By rebrendi
You mean that the former is...

You mean that the former is automatically+manually created, and the latter is manually created? Ok, but that does not answer my question.

I can not check each individual gene as I did in the...
Forum: Bioinformatics 03-03-2012, 06:36 AM
Replies: 31
Views: 4,828
Posted By rebrendi
Although, there is still something that I do not...

Although, there is still something that I do not understand:

For example, let's take the Ensemble mouse annotation: around 95,000 entries.

Now, let's look at some other database that contains...
Forum: Bioinformatics 03-03-2012, 05:31 AM
Replies: 31
Views: 4,828
Posted By rebrendi
Ok, great, thank you guys!

Ok, great, thank you guys!
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