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Search: Posts Made By: polivares
Forum: Literature Watch 03-02-2010, 04:22 AM
Replies: 1
Views: 1,672
Posted By polivares
The problem with this study is on how can you...

The problem with this study is on how can you fuse (in a clean way) the different sorted fractions to create a real timing profile .
Forum: Introductions 01-14-2010, 12:10 PM
Replies: 33
Views: 9,291
Posted By polivares
I want to thank you for the great tool you have...

I want to thank you for the great tool you have developed !

You make me save LOTS of time.

All the best :D

Pedro
Forum: Bioinformatics 01-14-2010, 09:55 AM
Replies: 1
Views: 2,406
Posted By polivares
Aren't chr23 and chr24 chrX and chrY ? I am...

Aren't chr23 and chr24 chrX and chrY ? I am facing a similar problem with some illumina data.
Forum: Bioinformatics 01-14-2010, 08:04 AM
Replies: 292
Views: 161,533
Posted By polivares
Hi, I am trying to find a script able to...

Hi,

I am trying to find a script able to convert from a output file from the solexa pipeline called 'realign' ( page 9 ...
Forum: Bioinformatics 10-29-2009, 02:30 AM
Replies: 1
Views: 1,754
Posted By polivares
You can generate a BED file of the binding sites...

You can generate a BED file of the binding sites of each sample. Then using overlapSelect from Jim Kents source tree you can generate a file with the overlapping regions. Then just with some simple...
Forum: Sample Prep / Library Generation 10-08-2009, 01:12 AM
Replies: 4
Views: 14,497
Posted By polivares
Thanks !!! Very interesting, I'll will chew it...

Thanks !!! Very interesting, I'll will chew it around and discuss it with chemists. I'll report if there is something to share.
Forum: Bioinformatics 10-06-2009, 12:49 PM
Replies: 3
Views: 8,004
Posted By polivares
From...

From http://www.broadinstitute.org/igv/doc/fileformats_TEXT.htm

IGV File Format

An IGV file (.igv) is a tab-delimited text file that defines tracks. The first row contains column headings for...
Forum: Illumina/Solexa 10-06-2009, 06:45 AM
Replies: 18
Views: 15,038
Posted By polivares
Hi, I would like to know the fragmentation size...

Hi,
I would like to know the fragmentation size spectrum of the covaris s2. Some resources state that the minimum size is around 600 bp but others state that it is 60 bp. Besides, does...
Forum: Bioinformatics 10-02-2009, 04:37 AM
Replies: 292
Views: 161,533
Posted By polivares
You can use wgsim from SAM tools which as far as...

You can use wgsim from SAM tools which as far as I understand is the "son" of mac simulate.
Forum: Bioinformatics 10-01-2009, 03:09 AM
Replies: 292
Views: 161,533
Posted By polivares
@jasonbcold I have not used jbrowse but I'd...

@jasonbcold
I have not used jbrowse but I'd recommend you to try IGV which can load indexed BAM alignments without any trouble. If you need some helo PM me.
Forum: Bioinformatics 09-24-2009, 12:05 PM
Replies: 292
Views: 161,533
Posted By polivares
http://seqanswers.com/forums/showthread.php?t=806

http://seqanswers.com/forums/showthread.php?t=806
Forum: Bioinformatics 09-23-2009, 09:05 AM
Replies: 3
Views: 8,004
Posted By polivares
I was struggling a bit while displaying big...

I was struggling a bit while displaying big tracks in UCSC Gbrowser. I found a better option to use the IGV genome browser than working remotely. I'd suggest the community to have a look on it.
...
Forum: General 09-23-2009, 09:00 AM
Replies: 30
Views: 14,846
Posted By polivares
Can someone please help me understand the...

Can someone please help me understand the parameters of wgsim. I am struggling to understand how changing the standard deviation [-s paramater; default value = 50] and the "outer distance between the...
Forum: Epigenetics 09-16-2009, 03:18 AM
Replies: 4
Views: 8,674
Posted By polivares
? nanopores?

? nanopores?
Forum: Epigenetics 08-30-2009, 10:06 AM
Replies: 4
Views: 8,674
Posted By polivares
What is the difference with methylated DNA? is it...

What is the difference with methylated DNA? is it the same thing?
Forum: Epigenetics 08-28-2009, 10:45 AM
Replies: 1
Views: 2,499
Posted By polivares
This is a complementary paper ...

This is a complementary paper

http://www.ncbi.nlm.nih.gov/pubmed/1...?dopt=Abstract
Forum: General 08-28-2009, 07:47 AM
Replies: 8
Views: 8,217
Posted By polivares
:):):):):):):):):)

:):):):):):):):):)
Forum: Literature Watch 08-28-2009, 07:45 AM
Replies: 0
Views: 1,575
Posted By polivares
Mapping accessible chromatin regions using Sono-Seq.

Proc Natl Acad Sci U S A. 2009 Aug 18. [Epub ahead of print]

Mapping accessible chromatin regions using Sono-Seq.

Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z,...
Forum: General 08-26-2009, 08:47 AM
Replies: 8
Views: 8,217
Posted By polivares
Anyway I would recommend to visit it directly

Anyway I would recommend to visit it directly
Forum: Illumina/Solexa 08-25-2009, 09:18 AM
Replies: 18
Views: 6,183
Posted By polivares
I would run different trials with tools like this...

I would run different trials with tools like this (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) with different window sizes helping me a bit with the known splicing sites :S
Forum: Illumina/Solexa 08-25-2009, 07:58 AM
Replies: 18
Views: 6,183
Posted By polivares
Do you think that there may be some non-random...

Do you think that there may be some non-random distribution of how RNA breaks in any sample determined by secondary structure? In other words, can you find any correlation between you bias that may...
Forum: General 08-25-2009, 03:32 AM
Replies: 8
Views: 8,217
Posted By polivares
Mapability or "why my mapping is biased?"

I found this track a very important piece of information to have in mind while mapping reads to the human genome. To be honest I have not found it discussed that much out there (I may be wrong :p). I...
Forum: Illumina/Solexa 08-25-2009, 03:28 AM
Replies: 18
Views: 6,183
Posted By polivares
The genome has repeated sequences. So if you plot...

The genome has repeated sequences. So if you plot the "uniqueness" of the genome in a n-sized window you'll find how mappable that region of the genome is for a set read length. It is important to...
Forum: Bioinformatics 08-01-2009, 12:25 PM
Replies: 7
Views: 6,024
Posted By polivares
As wikipedia's article...

As wikipedia's article (http://en.wikipedia.org/wiki/FASTQ_format#NCBI_Short_Read_Archive) states, SRA files are already in Sanger's qualities. You should only remove the spaces. Please tell me if I...
Forum: Bioinformatics 08-01-2009, 11:07 AM
Replies: 3
Views: 3,501
Posted By polivares
Too add an option I'd recommend to patch maq with...

Too add an option I'd recommend to patch maq with : this patch (http://sourceforge.net/tracker/index.php?func=detail&aid=2824334&group_id=191815&atid=938893)
hope it's helpful
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