Forum: Pacific Biosciences
12-19-2018, 07:26 AM
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Replies: 0
Views: 2,627
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...
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Forum: Bioinformatics
12-17-2018, 10:52 AM
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Replies: 0
Views: 920
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...
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Forum: Pacific Biosciences
04-06-2018, 06:48 AM
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Replies: 0
Views: 2,065
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...
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Forum: Epigenetics
08-23-2017, 12:05 PM
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Replies: 0
Views: 5,223
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...
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Forum: Bioinformatics
03-17-2017, 02:53 PM
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Replies: 0
Views: 1,293
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...
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Forum: Bioinformatics
07-08-2016, 02:33 PM
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Replies: 2
Views: 1,299
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Forum: Bioinformatics
06-23-2016, 01:32 PM
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Replies: 2
Views: 1,299
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...
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Forum: Bioinformatics
03-16-2016, 11:09 AM
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Replies: 0
Views: 736
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...
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Forum: Epigenetics
01-27-2016, 12:12 PM
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Replies: 0
Views: 1,512
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
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Forum: Epigenetics
01-15-2016, 11:32 AM
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Replies: 3
Views: 2,245
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...
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Forum: Epigenetics
01-14-2016, 11:37 AM
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Replies: 3
Views: 7,323
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...
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Forum: Pacific Biosciences
11-06-2015, 02:51 PM
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Replies: 8
Views: 2,701
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Forum: Pacific Biosciences
11-06-2015, 02:44 PM
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Replies: 8
Views: 2,701
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Forum: Pacific Biosciences
11-04-2015, 03:11 PM
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Replies: 8
Views: 2,701
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Forum: Pacific Biosciences
11-03-2015, 09:45 AM
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Replies: 8
Views: 2,701
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...
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Forum: Pacific Biosciences
09-17-2015, 08:28 AM
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Replies: 0
Views: 1,171
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...
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Forum: General
06-24-2015, 08:25 AM
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Replies: 1
Views: 1,171
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...
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Forum: Pacific Biosciences
05-26-2015, 07:10 AM
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Replies: 15
Views: 3,482
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...
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Forum: Pacific Biosciences
05-26-2015, 07:02 AM
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Replies: 8
Views: 2,726
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Forum: Pacific Biosciences
05-20-2015, 01:42 PM
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Replies: 8
Views: 2,726
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Forum: Pacific Biosciences
05-20-2015, 11:45 AM
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Replies: 8
Views: 2,726
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Forum: Pacific Biosciences
05-20-2015, 08:08 AM
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Replies: 8
Views: 2,726
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...
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Forum: Pacific Biosciences
05-12-2015, 04:20 PM
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Replies: 15
Views: 3,482
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Forum: Pacific Biosciences
05-12-2015, 07:59 AM
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Replies: 15
Views: 3,482
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...
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Forum: Pacific Biosciences
05-11-2015, 02:11 PM
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Replies: 15
Views: 3,482
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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