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Forum: Pacific Biosciences 04-28-2015, 04:29 PM
Replies: 7
Views: 2,509
Posted By SillyPoint
rhall, while we're on the subject of controls... ...

rhall, while we're on the subject of controls...

At what point are the control reads identified and removed from the data stream? Is that done during the processing on the instrument? Are the...
Forum: Pacific Biosciences 01-17-2014, 10:14 AM
Replies: 10
Views: 5,858
Posted By SillyPoint
Nice work, rhall. But I'd make this...

Nice work, rhall.

But I'd make this observation: Monika and every other user still have the problem that the protocol files supplied with smrtanalysis can't be passed directly to smrtpipe: They...
Forum: Pacific Biosciences 10-01-2013, 02:01 PM
Replies: 3
Views: 3,184
Posted By SillyPoint
As to hardware, the old answer applies: As much...

As to hardware, the old answer applies: As much as you can afford.

But I do have one possibly useful recommendation, if you are building a brand new cluster: Run it under SGE. PacBio claims to...
Forum: Bioinformatics 09-20-2013, 01:49 PM
Replies: 10
Views: 4,736
Posted By SillyPoint
I gather samtools calmd ran to completion then?...

I gather samtools calmd ran to completion then? That's too bad -- I was hoping it would blow up when it got to the bad read.

As to the example you posted: The SAM lines themselves look consistent....
Forum: Bioinformatics 09-19-2013, 02:54 PM
Replies: 10
Views: 4,736
Posted By SillyPoint
Sorry, mgaldos (and SEQquestions). I didn't mean...

Sorry, mgaldos (and SEQquestions). I didn't mean the AWK code is incomprehensible. I was talking about the code in bam_pileup.c where the exception occurred!

However, I worry about the AWK...
Forum: Bioinformatics 09-18-2013, 03:57 PM
Replies: 10
Views: 4,736
Posted By SillyPoint
Mgaldos, The code is incomprehensible. But...

Mgaldos,

The code is incomprehensible. But it looks like we're running off the end of the cigar string. You imply that it takes a while to fail, so it sounds like there is one read in there...
Forum: Bioinformatics 07-11-2012, 04:22 AM
Replies: 11
Views: 8,379
Posted By SillyPoint
How did it get that way?

Assuming the bowtie2 error messages speak the truth (which you can verify by examining the relevant fastq lines), I'd sure recommend tracing the problem back to its source, rather than trying to...
Forum: Pacific Biosciences 03-14-2012, 01:21 PM
Replies: 1
Views: 2,768
Posted By SillyPoint
Bug fix for PacBioEDA

I've just uploaded (link in OP) a fix to PacBioEDA for a bug which caused PacBio_Bas.py to print reference chromosome/contig numbers which do not reflect the order of the chrs in the reference file....
Forum: The Pipeline 02-21-2012, 08:21 AM
Replies: 0
Views: 5,302
Posted By SillyPoint
ONT error model and quality scoring

Regarding ONT's new technology, I think I heard the following over the last few days (please correct if I've mis-heard):


Error rate is 4% today, targeting 1% by release.

Predominant error...
Forum: The Pipeline 02-20-2012, 08:19 AM
Replies: 8
Views: 5,569
Posted By SillyPoint
OK, I'll be sure to RTFM next time. But, judging...

OK, I'll be sure to RTFM next time. But, judging by recent events, ...

Either... This section will be swamped in the near term with ONT-related postings.

Or... ONT will announce the commercial...
Forum: The Pipeline 02-20-2012, 05:26 AM
Replies: 8
Views: 5,569
Posted By SillyPoint
Question When does a company graduate?

Hi ECO,

When does a company graduate from The Pipeline, and warrant a section of its own? I ask this relative to ONT, of course -- but GnuBio and LaserGen have stuck their heads above the parapet...
Forum: The Pipeline 02-01-2012, 10:59 AM
Replies: 103
Views: 141,608
Posted By SillyPoint
the most honest guy in sequencing

@nickloman: Clive Brown is speaking though - "the most honest guy in sequencing".

I'd think perhaps 'blunt' would be a better description :D.

Per @SeqAA: getting people out of their happy...
Forum: Pacific Biosciences 01-27-2012, 09:58 AM
Replies: 50
Views: 23,664
Posted By SillyPoint
AFAIK, any ascii-encoded Q scores in fastq or SAM...

AFAIK, any ascii-encoded Q scores in fastq or SAM files will be encoded Q+33.

See last post for caveats about quality scores, however.

--TS
Forum: Pacific Biosciences 01-26-2012, 10:35 AM
Replies: 50
Views: 23,664
Posted By SillyPoint
Actually, the answer to rghan's "question...

Actually, the answer to rghan's "question regarding quality scores" is tougher than it looks. First off, it depends on what you want the fastq file to contain.

If you're after the circular...
Forum: Pacific Biosciences 01-17-2012, 08:00 AM
Replies: 50
Views: 23,664
Posted By SillyPoint
There's a high-level how-to...

There's a high-level how-to (http://www.pacbiodevnet.com/Learn/How-To/E-coli-O104-Assembly) on pacbiodevnet, describing how they used a combination of consensus and long reads to do de novo assembly...
Forum: Illumina/Solexa 01-12-2012, 09:54 AM
Replies: 3
Views: 6,096
Posted By SillyPoint
I can do the easy one: It sounds like you...

I can do the easy one:

It sounds like you have one lane's worth of data. A HiSeq lane is processed as 48 tiles.

I haven't heard the term 'pseudotiles', but I'm guessing that just refers to the...
Forum: Pacific Biosciences 01-10-2012, 09:43 AM
Replies: 1
Views: 2,768
Posted By SillyPoint
PacBioEDA: Exploratory Data Analysis tools for PacBio RS

I've just posted to github PacBioEDA (https://github.com/TomSkelly/PacBioEDA), a package of python scripts for subread-level examination of the output of the PacBio instrument.

From the blurb (on...
Forum: Illumina/Solexa 11-26-2010, 10:32 AM
Replies: 4
Views: 3,353
Posted By SillyPoint
You should also be aware of the (relatively) new...

You should also be aware of the (relatively) new SAM/BAM format. It (optionally) includes alignment information, in addition to sequence and quality. There are lots of tools for manipulating data in...
Forum: Bioinformatics 10-26-2010, 09:55 AM
Replies: 9
Views: 3,544
Posted By SillyPoint
To paraphase Mr Gates, "192GB oughta be enough...

To paraphase Mr Gates, "192GB oughta be enough for anybody." Can't believe you're paging with that much RAM.

--TS
Forum: Bioinformatics 10-26-2010, 06:48 AM
Replies: 9
Views: 3,544
Posted By SillyPoint
Paging?

In the situation you describe, I'd be a little suspicious about memory usage and paging. Because the tiles are 10 times larger, the Illumina pipeline uses a lot more memory for a HiSeq run than for...
Forum: Illumina/Solexa 07-07-2010, 10:41 AM
Replies: 2
Views: 6,494
Posted By SillyPoint
Another phenomenon at work here is what Illumina...

Another phenomenon at work here is what Illumina calls 'phasing'. Remember that each cluster contains ~1000 (supposedly) identical molecules, all of which are undergoing reverse-strand synthesis.
...
Forum: Bioinformatics 04-06-2010, 04:32 AM
Replies: 5
Views: 5,379
Posted By SillyPoint
Hi Charles, What version of CMAKE did you...

Hi Charles,

What version of CMAKE did you install? The problem described by Sanzi occurred with a fairly recent version.

--SP
Forum: Illumina/Solexa 01-27-2010, 11:10 AM
Replies: 5
Views: 8,937
Posted By SillyPoint
We've had control lane PhiX samples from a couple...

We've had control lane PhiX samples from a couple of different sources, including Illumina and home-grown. We do see a few differences, which isn't surprising.

One batch featured a single...
Forum: Bioinformatics 01-20-2010, 11:25 AM
Replies: 513
Views: 205,638
Posted By SillyPoint
I'd just logged on here to post exactly the...

I'd just logged on here to post exactly the question acnoll poses above: "is it possible to have pairs with only one end mapping to the genome be included in the alignment file?"

The implication...
Forum: Bioinformatics 01-13-2010, 12:10 PM
Replies: 5
Views: 5,379
Posted By SillyPoint
Looking at my 1.5.0 install output, I see that it...

Looking at my 1.5.0 install output, I see that it installed its own copy of cmake, version 2.6.2. Yours found an existing cmake, version 2.6-patch 2.

About 10 lines down in your output, cmake is...
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