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Forum: Pacific Biosciences 02-12-2019, 08:22 AM
Replies: 6
Views: 1,980
Posted By rhall
If you assemble a set of reads, then use them to...

If you assemble a set of reads, then use them to polish the assembly, there is no way to measure any truly meaningful consensus quality without an orthogonal datatype, or knowledge of ground truth....
Forum: Pacific Biosciences 04-11-2018, 07:35 AM
Replies: 1
Views: 2,261
Posted By rhall
It's possible that ploidy could account for some...

It's possible that ploidy could account for some of the difference, but it is unlikely that it is that simple. Using default parameters I wouldn't expect Canu to not collapse haplotypes and Falcon to...
Forum: Pacific Biosciences 03-20-2018, 08:29 AM
Replies: 6
Views: 3,326
Posted By rhall
The data looks a little overloaded, but for...

The data looks a little overloaded, but for sequel these number do not look unreasonable.
The mean subread size does look low, but given a 15kb size selection, it's within expectations. Was there...
Forum: Pacific Biosciences 01-31-2018, 02:04 PM
Replies: 3
Views: 2,857
Posted By rhall
Can you try on the command line pbservice...

Can you try on the command line
pbservice import-dataset --host <hostname> --port <port> m54113_160914_092411.subreadset.xml --verbose
Forum: Pacific Biosciences 01-30-2018, 07:54 AM
Replies: 3
Views: 2,857
Posted By rhall
For a quick resolution, file a ticket with Pacbio...

For a quick resolution, file a ticket with Pacbio tech support.

Alternatively, what version of SMRT Link are you using, and where did the data come from?
Forum: Pacific Biosciences 01-15-2018, 11:05 AM
Replies: 6
Views: 3,326
Posted By rhall
The P1 is high, probably a sign of overloading....

The P1 is high, probably a sign of overloading. This results in low quality data, and limited subread lengths.
It's always worth assembling the data, even if the raw data isn't of the absolute...
Forum: Pacific Biosciences 01-11-2018, 09:39 AM
Replies: 6
Views: 3,326
Posted By rhall
The subread statistics are the important numbers...

The subread statistics are the important numbers for assembly. You should have enough coverage in the subread bases, and good subread mean / N50 readlingth.

The subread stats will depend on the...
Forum: Pacific Biosciences 11-28-2017, 12:13 PM
Replies: 5
Views: 2,987
Posted By rhall
Preassembled yield, polished contig total size...

Preassembled yield, polished contig total size and what the raw coverage of the polished contigs is would be a good place to start.
Forum: Pacific Biosciences 11-27-2017, 08:55 AM
Replies: 4
Views: 2,459
Posted By rhall
While a kmer analysis is going to be difficult...

While a kmer analysis is going to be difficult with the raw pacbio data, it is possible to estimate the (effective) genome size from overlap statistics, either for the raw reads, the error corrected...
Forum: Pacific Biosciences 11-27-2017, 08:47 AM
Replies: 5
Views: 2,987
Posted By rhall
HGAP.4, it's actually not possible to run sequel...

HGAP.4, it's actually not possible to run sequel data through the HGAP.2 and HGAP.3 pipelines.
How big is the fungi? so long as you have reasonable coverage default parameters should be a good...
Forum: Pacific Biosciences 09-19-2017, 08:02 AM
Replies: 7
Views: 2,581
Posted By rhall
The run looks reasonably good. There are 1593...

The run looks reasonably good. There are 1593 control reads i.e. its only a very small portion of your data (as it should be), and the polymerase read length and concordance for the control look...
Forum: Pacific Biosciences 09-05-2017, 08:05 AM
Replies: 7
Views: 2,581
Posted By rhall
See the attached PDF.

See the attached PDF.
Forum: Pacific Biosciences 05-24-2017, 08:24 AM
Replies: 2
Views: 2,160
Posted By rhall
I'm not an expert, but on asking some people who...

I'm not an expert, but on asking some people who should know, the response was - "If it didn't sit at room temperature for any extended period of time it should be OK, but it's not something we have...
Forum: Pacific Biosciences 05-18-2017, 09:10 AM
Replies: 2
Views: 1,447
Posted By rhall
While it isn't as simple as looking for circular...

While it isn't as simple as looking for circular bacterial chromosomes, if you know the number of chromosomes and rough size distribution you should be able to estimate how complete your assembly is....
Forum: Pacific Biosciences 05-08-2017, 09:02 AM
Replies: 9
Views: 2,277
Posted By rhall
There will be significant noise in this analysis...

There will be significant noise in this analysis and I wouldn't expect all subreads to perform the same with regards to the alignment.

Running ROI with 0 passes and minimum quality of 0 is not a...
Forum: Pacific Biosciences 05-04-2017, 12:53 AM
Replies: 9
Views: 2,277
Posted By rhall
There is no need to run circular consensus for...

There is no need to run circular consensus for denovo genome assembly or scaffolding, the power in the data is in the read length, not in the base accuracy, and calculating CCS drastically reduces...
Forum: Pacific Biosciences 04-06-2017, 10:10 AM
Replies: 2
Views: 1,650
Posted By rhall
It is possible that the data is from a population...

It is possible that the data is from a population that is not perfectly clonal. This happens frequently in slow growing organisms, or things that mutate rapidly.
Forum: Pacific Biosciences 04-04-2017, 09:02 AM
Replies: 4
Views: 1,706
Posted By rhall
Which version of SMRT Tools are you considering...

Which version of SMRT Tools are you considering installing? The latest versions should have no problem installing on Ubuntu 14.04.
Forum: Pacific Biosciences 04-04-2017, 08:56 AM
Replies: 2
Views: 1,336
Posted By rhall
Are all the amplicons from distinct regions, or...

Are all the amplicons from distinct regions, or are they overlapping?
The first thing I would try is to run LAA, but only on a single amplicon at a time, that way the coarse clustering is...
Forum: Pacific Biosciences 04-04-2017, 08:45 AM
Replies: 1
Views: 2,108
Posted By rhall
Hi, There isn't one well developed approach to...

Hi,
There isn't one well developed approach to an experiment like this, I can think of a lot of things to try, but it is going to come down to a lot of manual assembly work.
My first observation...
Forum: Pacific Biosciences 03-23-2017, 09:38 AM
Replies: 4
Views: 1,578
Posted By rhall
LAA should be able to deal with the fragmented...

LAA should be able to deal with the fragmented data, so long as there are reasonable number of full length sequences.
Forum: Pacific Biosciences 03-23-2017, 07:09 AM
Replies: 4
Views: 1,578
Posted By rhall
How long is the PCR product? LAA would be the...

How long is the PCR product? LAA would be the recommendation if the insert size is too long to get a high CCS (ROI) yield >3kb ish.
Do the shorter fragments have both barcodes? How were the barcodes...
Forum: Bioinformatics 03-14-2017, 02:37 PM
Replies: 0
Views: 816
Posted By rhall
SMRT Leiden Conference: May 2 - 4, 2017 SMRT Scientific Symposium & Developers Mtg

Register now (http://www.lgtc.nl/SMRTLeiden/) for the 2nd annual SMRT Leiden Conferences, bringing together the SMRT community for three days of engaging science and networking at the Leiden...
Forum: Pacific Biosciences 01-23-2017, 01:37 PM
Replies: 2
Views: 1,791
Posted By rhall
Sequel data does not have a per base QV value for...

Sequel data does not have a per base QV value for raw reads. If you calculate CCS first then the quality values will be meaningfully populated.
Forum: Pacific Biosciences 12-16-2016, 10:19 AM
Replies: 17
Views: 7,561
Posted By rhall
FYI, the scraps file includes all the sequence...

FYI, the scraps file includes all the sequence not in the HQ (high quality) region, and the adapter sequences. The old bax format saved everything with indexes into the usable data. The subreads.bam...
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