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Search: Posts Made By: gconcepcion
Forum: Pacific Biosciences 10-31-2017, 02:41 PM
Replies: 4
Views: 684
Posted By gconcepcion
Hi Zapp, I'm currently involved in a project...

Hi Zapp,

I'm currently involved in a project where we are doing just that, using sperm DNA for denovo assembly in FALCON. It's not my project, so I can't go into the details, i'm simply helping on...
Forum: Bioinformatics 10-17-2017, 02:28 PM
Replies: 4
Views: 628
Posted By gconcepcion
Why not use `bwa` to map the raw reads back to...

Why not use `bwa` to map the raw reads back to the reference?

$ bwa index reference.fasta
$ bwa mem -x pacbio -t 24 reference.fasta raw_subreads.fasta >output.sam


then sort, index and open...
Forum: Pacific Biosciences 04-06-2017, 11:07 AM
Replies: 2
Views: 844
Posted By gconcepcion
Hi dladuswj, It seems likely that the...

Hi dladuswj,

It seems likely that the bacterial genome that you are sequencing contains more/longer homopolymer/repetitive regions than the typical genomes you are sequencing, which could result...
Forum: Pacific Biosciences 04-05-2017, 01:57 PM
Replies: 4
Views: 1,193
Posted By gconcepcion
I have installed smrtlink on my personal Ubuntu...

I have installed smrtlink on my personal Ubuntu 14.04 laptop and it works fine. I haven't tried it on 16.04, but I can't think of any reasons off the top of my head why it wouldn't work.
Forum: Pacific Biosciences 03-06-2017, 12:50 PM
Replies: 4
Views: 1,193
Posted By gconcepcion
Hi Michael, You have two options: 1)...

Hi Michael,

You have two options:
1) Contact your service provider and obtain the original *.bas.h5 files
2) Use FALCON to assemble your genome from *.fasta files. FALCON is essentially the...
Forum: Pacific Biosciences 12-19-2016, 04:31 PM
Replies: 15
Views: 4,009
Posted By gconcepcion
$ ls *.subreads.bam >input.fofn $ pbalign...

$ ls *.subreads.bam >input.fofn
$ pbalign --nproc 32 input.fofn Q1133.092116.GS170M.contigs.fasta Q1133.aligned.bam


pbalign takes individual sequence files as input, or a File of File Names...
Forum: Pacific Biosciences 11-18-2016, 09:04 AM
Replies: 8
Views: 2,462
Posted By gconcepcion
Heterozygosity is a real issue for assembling...

Heterozygosity is a real issue for assembling data from any technology, not just pacbio. this is likely to be an issue with any multi-isolate algal culture. The best way for algae is to do...
Forum: Pacific Biosciences 11-18-2016, 08:58 AM
Replies: 21
Views: 4,877
Posted By gconcepcion
What issue are you having with samtools? the...

What issue are you having with samtools?

the new SEQUEL *.bam files are 100% compatible with samtools, we routinely use it internally and it's included as part of SMRTLink
Forum: Pacific Biosciences 11-15-2016, 11:48 AM
Replies: 8
Views: 2,462
Posted By gconcepcion
One way to circumvent this is with the...

One way to circumvent this is with the overlap_filtering_setting in FALCON. This allows you to filter out "chimeric contigs" due to the fact that overlap coverage will differ across the contig. The...
Forum: Pacific Biosciences 10-28-2016, 10:07 AM
Replies: 3
Views: 1,028
Posted By gconcepcion
If you can shed some light on what you are trying...

If you can shed some light on what you are trying to do, and what data you have to start with, it will make it easier for people to help you.

Now I understand that you are trying to scaffold short...
Forum: Pacific Biosciences 10-28-2016, 09:07 AM
Replies: 3
Views: 1,028
Posted By gconcepcion
With low coverage data, you will barely be able...

With low coverage data, you will barely be able to assemble a decent un-separated (haploid) assembly. Typically we recommend about 60X coverage for haploid assembly, and twice that for diploid...
Forum: Pacific Biosciences 09-16-2016, 10:19 AM
Replies: 5
Views: 1,587
Posted By gconcepcion
This is characteristic of a loading issue as...

This is characteristic of a loading issue as rhall indicated.

Unfortunately the ReadsOfInsert protocols don't give you the loading report information, however you can lump all of the cells...
Forum: Pacific Biosciences 09-09-2016, 09:39 AM
Replies: 4
Views: 1,246
Posted By gconcepcion
Again, MatchAnnot was written by a third party...

Again, MatchAnnot was written by a third party developer, your question would be better addressed to the author of the software as an issue in the github page I linked in my first post.

This...
Forum: Pacific Biosciences 09-07-2016, 09:53 AM
Replies: 4
Views: 1,246
Posted By gconcepcion
This is really a question for the author of the...

This is really a question for the author of the software, MatchAnnot, Tom Skelly.

https://github.com/TomSkelly/MatchAnnot

Without seeing your annotations dataset, all I can say is make sure the...
Forum: Pacific Biosciences 08-30-2016, 08:03 AM
Replies: 2
Views: 911
Posted By gconcepcion
The numbers are in the first column - ...

The numbers are in the first column -

Productivity-0: 21870 / 150292 total = 14.6%
Productivity-1: 80606 / 150292 total = 53.6%
Productivity-2: 47816 / 150292 total = 31.8%
Forum: Pacific Biosciences 08-22-2016, 01:17 PM
Replies: 8
Views: 1,226
Posted By gconcepcion
How long are the two contigs? Is one roughly 4Kb?...

How long are the two contigs? Is one roughly 4Kb? The SMRTCell internal control is not removed by the HGAP assembly process, and may be what you are seeing - see this thread:...
Forum: Pacific Biosciences 08-17-2016, 10:09 AM
Replies: 8
Views: 1,226
Posted By gconcepcion
Sorry, I'm not sure exactly what you mean by...

Sorry, I'm not sure exactly what you mean by "fully" supported.

The last time I tested and used SMRTanalysis 2.3.0 with LSF was sometime late last year to run some basic integration tests, and...
Forum: Pacific Biosciences 08-17-2016, 09:58 AM
Replies: 8
Views: 1,226
Posted By gconcepcion
OK, that's plenty of coverage, that's not the...

OK, that's plenty of coverage, that's not the issue.



Who installed smrtanalysis for you? Make sure CLUSTER_MANAGER=LSF is in the smrtpipe.rc file located here:
...
Forum: Pacific Biosciences 08-16-2016, 03:02 PM
Replies: 8
Views: 1,226
Posted By gconcepcion
I see you have the genomeSize set @ 124kb, how...

I see you have the genomeSize set @ 124kb, how much input coverage do you have?

If you can zip up the rest of the logs (particularly the ones in log/P_PreAssemblerDagcon/*) it will facilitate the...
Forum: Pacific Biosciences 08-15-2016, 09:35 AM
Replies: 3
Views: 2,935
Posted By gconcepcion
Q50 implies that there is on average 1 error in a...

Q50 implies that there is on average 1 error in a 100,000bp stretch when aligning a consensus sequences to a reference.

See the wikipedia entry on phred score here:...
Forum: Pacific Biosciences 08-05-2016, 01:24 PM
Replies: 2
Views: 831
Posted By gconcepcion
sh: qsub: not found This indicates that...

sh: qsub: not found


This indicates that the SGE binaries are not in your $PATH.

I'm assuming you're trying to run it locally on an AWS server, and not through SGE.

Try setting the option...
Forum: Pacific Biosciences 07-29-2016, 01:31 PM
Replies: 10
Views: 1,440
Posted By gconcepcion
There appear to be blank lines in your *.fofn's ...

There appear to be blank lines in your *.fofn's

Try removing the blank lines at the end and re-running.
Forum: Pacific Biosciences 07-28-2016, 06:43 AM
Replies: 10
Views: 1,440
Posted By gconcepcion
It seems as though pulse features were not added...

It seems as though pulse features were not added into your *.cmp.h5

What was the process you used to generate your cmp.h5. Did you use pbalign with the --forQuiver option?
Forum: Bioinformatics 07-27-2016, 10:23 AM
Replies: 5
Views: 1,471
Posted By gconcepcion
If you would like direct assistance from the...

If you would like direct assistance from the developers, you should visit the FALCON github page:

https://github.com/PacificBiosciences/FALCON/issues

But in short, you *are* running locally,...
Forum: Pacific Biosciences 07-21-2016, 10:31 AM
Replies: 6
Views: 818
Posted By gconcepcion
Just to clarify, internally we refer to this as a...

Just to clarify, internally we refer to this as a "Concordance QV", not an "Accuracy QV". You are calculating how well a particular sequence "concords" with a particular reference sequence. Using the...
Showing results 1 to 25 of 67

 


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