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Search: Posts Made By: inesdesantiago
Forum: Bioinformatics 07-24-2014, 04:44 AM
Replies: 1
Views: 1,610
Posted By inesdesantiago
Actually, the reverse complement of the first...

Actually, the reverse complement of the first barcode worked.
I decided to allow only 1 mismatch now

Barcode1 output
Barcode Count Location
C52_1 166119 SRR342054_1rev_C52_1.fastq...
Forum: Bioinformatics 07-24-2014, 01:15 AM
Replies: 5
Views: 1,338
Posted By inesdesantiago
Hi luc, In which ocasions should one use the...

Hi luc,
In which ocasions should one use the reverse complement?
I am looking at demultiplexing some data, and there are NO reads matching my barcodes. When I run FASTQC it seams like there are...
Forum: Bioinformatics 07-24-2014, 01:01 AM
Replies: 1
Views: 1,610
Posted By inesdesantiago
Demultiplexing 454

Dear all,
I am trying to de-multiplex a 454 fasta file.

It is a public data file. In the paper (PMID:21731642 (http://www.ncbi.nlm.nih.gov/pubmed/21731642)) the authors say that:
"The HB4a and...
Forum: Bioinformatics 06-30-2014, 05:03 AM
Replies: 16
Views: 12,292
Posted By inesdesantiago
You could also use GenomeIntervals2BED.py script...

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
Forum: Bioinformatics 06-30-2014, 05:02 AM
Replies: 7
Views: 6,565
Posted By inesdesantiago
You could also use GenomeIntervals2BED.py script...

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
Forum: Bioinformatics 06-30-2014, 05:02 AM
Replies: 2
Views: 10,545
Posted By inesdesantiago
You could also use GenomeIntervals2BED.py script...

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
Forum: Bioinformatics 06-30-2014, 05:01 AM
Replies: 57
Views: 38,186
Posted By inesdesantiago
You could also use GenomeIntervals2BED.py script...

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
Forum: Bioinformatics 02-27-2013, 08:20 AM
Replies: 8
Views: 3,496
Posted By inesdesantiago
Hello. Looking at different classes of repeats,...

Hello.
Looking at different classes of repeats, it seems like satellite repeats are enriched in the lower arm. Also quite common in the Y chromosome.
Thanks!
ines
Forum: Bioinformatics 02-26-2013, 03:11 PM
Replies: 8
Views: 3,496
Posted By inesdesantiago
Good point.. The chrY shows the negative regions,...

Good point.. The chrY shows the negative regions, and they correspond to the lower arm of the plot.
Thanks!
Forum: Bioinformatics 02-26-2013, 11:16 AM
Replies: 8
Views: 3,496
Posted By inesdesantiago
Hello pmcget, These are T47D cells, a human...

Hello pmcget,
These are T47D cells, a human breast cancer cell line, and the Transcription factor is FOXA1 ChIP-Seq.
I have checked a few peaks with the track "repeat masker", and I didn't find...
Forum: Bioinformatics 02-26-2013, 05:32 AM
Replies: 8
Views: 3,496
Posted By inesdesantiago
Hello pmcget, I tried the same plot with and...

Hello pmcget,
I tried the same plot with and without replicates. The one I posted is without duplicates, which I removed using picard.

I donít think the code has any error. I tried the same code...
Forum: Bioinformatics 02-26-2013, 02:49 AM
Replies: 8
Views: 3,496
Posted By inesdesantiago
"Offset" in the correlation between two ChIP-seq biological replicates

Hello.
I was looking at the correlation of signal intensities between two biological replicates (ChIP-Seq) and I got a strange plot. I was wondering if anyone has seen something like this before, or...
Forum: Bioinformatics 12-14-2009, 04:01 PM
Replies: 2
Views: 1,459
Posted By inesdesantiago
Hi dawe! Thanks for the reply! I tried with...

Hi dawe!
Thanks for the reply! I tried with your last suggestions

$comm = "qsub -S /bin/sh -l walltime=48:00:00 -o $mysh.out -e $mysh.err $mysh > $mysh.id ";


and it worked perfectly. I would...
Forum: Bioinformatics 12-04-2009, 04:38 PM
Replies: 2
Views: 1,459
Posted By inesdesantiago
RNA-MATE in an SGE queue manager

Hello
I am trying to use RNA-MATE in a computer cluster with an SGE queue manager. In RNA-MATE v1.1 user guide, the user is instructed to change a couple of things in the RNA-mapping.pm perl script....
Forum: SOLiD 10-05-2009, 09:28 AM
Replies: 35
Views: 21,440
Posted By inesdesantiago
That's a good idea, I haven't thought about...

That's a good idea, I haven't thought about mapping using colorspace...
To bad bowtie doesn't map with colorspace yet..
Regards,
Ines
Forum: SOLiD 10-05-2009, 09:24 AM
Replies: 35
Views: 21,440
Posted By inesdesantiago
Dear westerman, Thanks for the reply I...

Dear westerman,
Thanks for the reply

I have a collection of reads that are 35 nuc long.
In all of them there is a '.' in the same position, so when I translate from
colorspace to basesapce all...
Forum: SOLiD 10-05-2009, 09:22 AM
Replies: 35
Views: 21,440
Posted By inesdesantiago
Thanks for the reply I have a collection of...

Thanks for the reply

I have a collection of reads that are 35 nuc long.
In all of them there is a '.' in the same position, so when I translate from
colorspace to basesapce all of my reads...
Forum: SOLiD 10-05-2009, 06:54 AM
Replies: 34
Views: 28,029
Posted By inesdesantiago
Editing SOLiD2Std.pl to include more colorspace->basespace

Hi BENM

I edited your SOLid2Std.pl script to include some extra colorspace mapping code that was not considered originally.

I wanted to include the following basespace mapping:
Basically any...
Forum: SOLiD 10-05-2009, 06:38 AM
Replies: 35
Views: 21,440
Posted By inesdesantiago
"N" in basespace

How come NA, NC, NT, NG all have the same colorspace code '5'.
This means that once you have N for a given base you never know what is the next base? You don't know if it is A,G,C,T ...
Right?...
Forum: Bioinformatics 06-30-2009, 11:39 AM
Replies: 32
Views: 33,829
Posted By inesdesantiago
I would like to hear about the Chip-Seq Challenge...

I would like to hear about the Chip-Seq Challenge 2.0!
Forum: Bioinformatics 06-30-2009, 01:57 AM
Replies: 513
Views: 199,815
Posted By inesdesantiago
Thumbs up Hello, kcook, you illuminated me! Now...

Hello,



kcook, you illuminated me! Now I anderstand the -m 1 better!
Forum: RNA Sequencing 06-24-2009, 02:30 PM
Replies: 4
Views: 3,086
Posted By inesdesantiago
Thumbs down Cloonan et al

Hi n.cloonan,
And what about the files with raw data? I would like to compare my mappings with gene expression data.
(sorry about the icon, it is not the one I wanted, I thought it was a question...
Forum: Bioinformatics 06-23-2009, 03:57 AM
Replies: 236
Views: 569,385
Posted By inesdesantiago
How about those softwares for data analysis, like...

How about those softwares for data analysis, like CASAVA, SAMtools and FindFeatures?
Forum: Bioinformatics 06-16-2009, 05:48 PM
Replies: 513
Views: 199,815
Posted By inesdesantiago
Hi lh3, you are right. The speed is dependent on...

Hi lh3, you are right. The speed is dependent on the information it has to report.

For instance, I tried to run bowtie with the parameter -m set to 1 and it took 3hours, while previously it was...
Forum: Bioinformatics 06-16-2009, 05:45 PM
Replies: 513
Views: 199,815
Posted By inesdesantiago
Wink Faster search for Bowtie

Hi lh3, you are right. The speed is dependent on the information it has to report.

For instance, I tried to run bowtie with the parameter -m set to 1 and it took 3hours, while previously it was...
Showing results 1 to 25 of 44

 


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