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Forum: Pacific Biosciences 12-19-2018, 07:26 AM
Replies: 0
Views: 2,518
Posted By cascoamarillo
In-silico control

Hi,

Just a quick one: how can I generate an in-silico control for modification analysis with my genome and my PacBio reads? So it predicts the IPD using the local sequence context around the...
Forum: Bioinformatics 12-17-2018, 10:52 AM
Replies: 0
Views: 843
Posted By cascoamarillo
Where are the UTRs in Augustus?

OK, long story short; after training and prediction with WebAugustus, with "User set UTR prediction: true", I don't see them (UTRs) clearly in the gtf - gff files. Instead, you see this output (gff...
Forum: Pacific Biosciences 04-06-2018, 06:48 AM
Replies: 0
Views: 1,970
Posted By cascoamarillo
Process SMRT seq kinetic with AgIn

Hi all,

I have a problem with the installation/execution of this program, which process SMRT sequencing kinetic .csv files to predict regional methylation

https://github.com/hacone/AgIn

In...
Forum: Epigenetics 08-23-2017, 12:05 PM
Replies: 0
Views: 4,657
Posted By cascoamarillo
makeMetaGeneProfile.pl from HomerTools

Hello,
Just a quick question regarding the script makeMetaGeneProfile.pl from HomerTools, used for creating metagene profiles:
http://homer.ucsd.edu/homer/ngs/quantification.html

So it is...
Forum: Bioinformatics 03-17-2017, 02:53 PM
Replies: 0
Views: 1,236
Posted By cascoamarillo
TFR output alignment into fasta?

Hi There,
Does anyone know how to convert the output alignment results from Tandem repeat finder (https://tandem.bu.edu/trf/trf.html) into a fasta representation (fasta, clustal, etc...).

I have...
Forum: Bioinformatics 07-08-2016, 02:33 PM
Replies: 2
Views: 1,234
Posted By cascoamarillo
Thank you! OK, now stuck on step 3.....

Thank you!
OK, now stuck on step 3.....
Forum: Bioinformatics 06-23-2016, 01:32 PM
Replies: 2
Views: 1,234
Posted By cascoamarillo
REPET denovo BLASTER step

Hi,
I am troubleshooting the software REPET https://urgi.versailles.inra.fr/Tools/REPET , and I got to the step 2 of TEdenovo.py analysis:

In
TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 2 -s...
Forum: Bioinformatics 03-16-2016, 11:09 AM
Replies: 0
Views: 700
Posted By cascoamarillo
Find telomeric repeats in reference

Hi,
It is been a while since I have been working with this issue: search and annotate telomeric (interstitial) repeats in a draft reference genome. We know the sequence type of the repeat, two...
Forum: Epigenetics 01-27-2016, 12:12 PM
Replies: 0
Views: 1,440
Posted By cascoamarillo
Tools for PacBio Methylome??

Hi,
I'm wondering is there are any tools (like the ones for Chip-seq analysis) to "play" with the methylome from PacBio output (modifications file) other than the PacBio programs per se. Thanks
Forum: Epigenetics 01-15-2016, 11:32 AM
Replies: 3
Views: 2,130
Posted By cascoamarillo
Hi, If the protocol you follow keeps no strand...

Hi,
If the protocol you follow keeps no strand information of RNA ("unstreanded") then I think you should consider no orientation for counting; sum all 5'-3' and 3'-5' reads for the same features. I...
Forum: Epigenetics 01-14-2016, 11:37 AM
Replies: 3
Views: 6,669
Posted By cascoamarillo
Hi all, And what about MeDIP-seq (not...

Hi all,
And what about MeDIP-seq (not ChIP-seq)? I guess the answer would be the same, but what parameters keep/change?
I'm working on a Illumina IP library (50 bp SE) made after inmunoprecipitate...
Forum: Pacific Biosciences 11-06-2015, 02:51 PM
Replies: 8
Views: 2,636
Posted By cascoamarillo
Sorry, but one more question regarding MotifMaker...

Sorry, but one more question regarding MotifMaker analysis. So it's been created to identify motifs associated with DNA modification in prokaryotic genomes, though it's not clear (for me) if the...
Forum: Pacific Biosciences 11-06-2015, 02:44 PM
Replies: 8
Views: 2,636
Posted By cascoamarillo
Yep, it works! Thanks

Yep, it works! Thanks
Forum: Pacific Biosciences 11-04-2015, 03:11 PM
Replies: 8
Views: 2,636
Posted By cascoamarillo
It doesn't look like that. I picked the files...

It doesn't look like that. I picked the files from motifMaker-master
https://github.com/PacificBiosciences/MotifMaker
to use as test
motifMaker.sh -f...
Forum: Pacific Biosciences 11-03-2015, 09:45 AM
Replies: 8
Views: 2,636
Posted By cascoamarillo
Dear pacbio God Almighty, Please, let me...

Dear pacbio God Almighty,
Please, let me continue this post..... I'm trying to run MotifMaker; in the begining looks good:

(smrtanalysis-2.3.0) [resources]$ motifMaker.sh
Usage: MotifMaker...
Forum: Pacific Biosciences 09-17-2015, 08:28 AM
Replies: 0
Views: 1,127
Posted By cascoamarillo
SMARTVIEW java memory

Hi all,
Sorry to post this on the PacBio forum, but maybe someone has experience the same problem and can help me to solve it. I've also posted on linux-ubuntu forums without success.

I'm running...
Forum: General 06-24-2015, 08:25 AM
Replies: 1
Views: 1,138
Posted By cascoamarillo
After genome assembly...

...what to do?
Hi, I've been working a little with a large genome assembly (250Mb). I have Illumina and PacBio reads using diffrent approaches. At the end, used SPAdes assembly with Illumina data...
Forum: Pacific Biosciences 05-26-2015, 07:10 AM
Replies: 15
Views: 3,331
Posted By cascoamarillo
Hi guys, Let me continue this post with a...

Hi guys,
Let me continue this post with a question regarding CA output. In 9-terminator/ folder there is a summary of the assembly with Read Depth Histogram. There are contigs (consensus) with more...
Forum: Pacific Biosciences 05-26-2015, 07:02 AM
Replies: 8
Views: 2,621
Posted By cascoamarillo
I'm using SMRT portal. There's a explanation of...

I'm using SMRT portal.
There's a explanation of how this cluster is configure. Just copy/paste from the sys admin.
The basic configuration is a beowulf cluster consisting of a head node and a...
Forum: Pacific Biosciences 05-20-2015, 01:42 PM
Replies: 8
Views: 2,621
Posted By cascoamarillo
Thanks for the answers! I set first 32 and...

Thanks for the answers!

I set first 32 and after 16, sorry for the confusion.


Yes


Hope this is what you are asking for:
CentOS 6.5 1 @ 32*1024
Forum: Pacific Biosciences 05-20-2015, 11:45 AM
Replies: 8
Views: 2,621
Posted By cascoamarillo
Yes, this cluster uses SGE.

Yes, this cluster uses SGE.
Forum: Pacific Biosciences 05-20-2015, 08:08 AM
Replies: 8
Views: 2,621
Posted By cascoamarillo
installing SMRT Portal on a cluster

Me again,

So now, I've installed SMRT Portal on a better cluster, hoping to reduce time in computing. But during the installation process

bash smrtanalysis_2.3.0.140936.run -p...
Forum: Pacific Biosciences 05-12-2015, 04:20 PM
Replies: 15
Views: 3,331
Posted By cascoamarillo
It's running. Apparently, it has finished with...

It's running. Apparently, it has finished with overlapStoreBuild process and now is dealing with the correct-frags.
Forum: Pacific Biosciences 05-12-2015, 07:59 AM
Replies: 15
Views: 3,331
Posted By cascoamarillo
Thank you all! Wow, how do you know where are...

Thank you all!
Wow, how do you know where are those config files? Just set a bigger hard time. Anyway; it seems (de novo assembly with pacbio) is quite a long process. I place in parallel a subset...
Forum: Pacific Biosciences 05-11-2015, 02:11 PM
Replies: 15
Views: 3,331
Posted By cascoamarillo
So the scheduler is killing the job but we are...

So the scheduler is killing the job but we are not sure why it's being set. The job is being submitted with a "hard" resource list that includes the parameter h_rt=43200. This means the hard limit...
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