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Forum: Oxford Nanopore 10-27-2014, 07:16 AM
Replies: 47
Views: 14,271
Posted By nickloman
Actually Neil Hall wrote that, I was just hosting...

Actually Neil Hall wrote that, I was just hosting for him. And he changed his mind because he bought a PacBio ;)
Forum: Oxford Nanopore 09-28-2014, 05:13 AM
Replies: 47
Views: 14,271
Posted By nickloman
Hi robp-- Sadly the base caller is proprietary...

Hi robp-- Sadly the base caller is proprietary software and I am not aware of any documentation about how it works. It would be great if someone hot on HMMs and the Viterbi algorithm could try and...
Forum: Oxford Nanopore 09-27-2014, 10:58 AM
Replies: 47
Views: 14,271
Posted By nickloman
Just for the record, you do not need permission...

Just for the record, you do not need permission from Oxford Nanopore to release data after you self-certify the "burn-in" and I did not seek it. One of the reasons I took until September to release...
Forum: Illumina/Solexa 02-18-2014, 12:43 PM
Replies: 27
Views: 6,561
Posted By nickloman
Yes, we are too.

Yes, we are too.
Forum: Illumina/Solexa 02-18-2014, 12:42 PM
Replies: 16
Views: 8,422
Posted By nickloman
We've run much higher cluster densities and still...

We've run much higher cluster densities and still stayed within the performance spec for V3 kits which is >70% Q30. First off, report this run to Illumina and get the kit replaced. If this problems...
Forum: Bioinformatics 11-13-2013, 02:15 PM
Replies: 7
Views: 1,149
Posted By nickloman
Definitely PacBio, it's actually competitively...

Definitely PacBio, it's actually competitively priced with 454, perhaps cheaper. Try Duke University's quote generator: https://dugsim.net/
Forum: Bioinformatics 09-26-2013, 09:50 AM
Replies: 1
Views: 1,119
Posted By nickloman
Look into the bedtools package for easy ways to...

Look into the bedtools package for easy ways to do things like this:
https://code.google.com/p/bedtools/
Forum: Bioinformatics 09-25-2013, 01:58 AM
Replies: 4
Views: 2,184
Posted By nickloman
Cool Given the way you produce the multi FASTA file,...

Given the way you produce the multi FASTA file, isn't it already an alignment? You should be able to use phylogenetic software directly. FastTree is a good option. However I suspect your tree won't...
Forum: Bioinformatics 09-23-2013, 06:36 AM
Replies: 3
Views: 1,739
Posted By nickloman
Which assembler did you use? Some will output...

Which assembler did you use? Some will output this information in the FASTA header, or in a separate statistics file, in which case it is easy to write a script to extract the ones you want....
Forum: 454 Pyrosequencing 09-22-2013, 03:18 AM
Replies: 4
Views: 2,311
Posted By nickloman
Hard to predict exactly, but it sounds like...

Hard to predict exactly, but it sounds like something has gone wrong to me. Have you tried Roche's 454 gsAssembler (Newbler) ?
Forum: Bioinformatics 09-20-2013, 01:59 AM
Replies: 6
Views: 1,795
Posted By nickloman
I think that is the old Illumina 'qseq' format: ...

I think that is the old Illumina 'qseq' format:
http://allaboutbioinfo.blogspot.co.uk/2011/08/qseq-and-export-file-format-of-illumina.html
Forum: Illumina/Solexa 08-23-2013, 01:43 PM
Replies: 26
Views: 13,385
Posted By nickloman
The %A bias is very suggestive you are running...

The %A bias is very suggestive you are running off the end of the fragment, so you would need longer insert libraries to benefit from the longer reads.
Forum: Illumina/Solexa 08-16-2013, 01:12 AM
Replies: 2
Views: 1,274
Posted By nickloman
Thanks! I was beginning to think no-one was out...

Thanks! I was beginning to think no-one was out there ;) Unfortunately we binned the post-PCR plate rather hastily. Next time we will keep it.

We did try cleaning up the PAL using an AMPure...
Forum: Illumina/Solexa 08-12-2013, 04:36 AM
Replies: 2
Views: 1,274
Posted By nickloman
Rescuing a Nextera XT PAL?

We regularly perform 96 barcode Nextera XT and the results are usually pretty good. However the last run on the MiSeq gave us a cluster density of a bit less than 200k, and less than half of the...
Forum: Bioinformatics 07-16-2013, 05:54 AM
Replies: 5
Views: 1,657
Posted By nickloman
You might find these couple of shell commands...

You might find these couple of shell commands helpful:
https://gist.github.com/nickloman/3974107
Forum: Bioinformatics 07-15-2013, 12:47 PM
Replies: 3
Views: 669
Posted By nickloman
What is a pathogen?...

What is a pathogen? http://www.biomedcentral.com/1741-7007/10/6
Forum: Bioinformatics 06-26-2013, 10:51 AM
Replies: 3
Views: 1,105
Posted By nickloman
You could filter on mapping quality, e.g. by...

You could filter on mapping quality, e.g. by piping through samtools a la

bwa mem ref fastq1 fastq2 | samtools view -S -q30 -
Forum: General 06-04-2013, 08:10 AM
Replies: 1
Views: 1,196
Posted By nickloman
Yes, this is possible. Indeed, when you do...

Yes, this is possible. Indeed, when you do regular RNA-Seq you get a lot of rRNA sequence!
Forum: Bioinformatics 05-23-2013, 01:28 PM
Replies: 7
Views: 2,259
Posted By nickloman
If this is from libraries made with Nextera it...

If this is from libraries made with Nextera it may represent biases in incorporation sites favoured by the transposase. We see this phenomenon frequently and don't find it necessary to trim it.
Forum: Bioinformatics 04-03-2013, 03:36 AM
Replies: 3
Views: 1,244
Posted By nickloman
PLOS ONE, or ASM's new Genome Announcements...

PLOS ONE, or ASM's new Genome Announcements journal.
Forum: The Pipeline 03-07-2013, 10:16 AM
Replies: 80
Views: 186,251
Posted By nickloman
Just to note I added a clarification from Clive...

Just to note I added a clarification from Clive at the bottom of the post on that particular point...

Given that they are continuously screening new and better pores and that is in fact one of the...
Forum: Bioinformatics 03-05-2013, 07:32 AM
Replies: 1
Views: 796
Posted By nickloman
I would guess you are running up against a quota...

I would guess you are running up against a quota limit and your job is being killed by the shell. Try running ulimit -a and see whether there are strict user limits for your account. You may need to...
Forum: De novo discovery 01-17-2013, 08:16 AM
Replies: 9
Views: 2,038
Posted By nickloman
This is basically genomic 'dark matter' that is...

This is basically genomic 'dark matter' that is impossible to assemble de novo right now from shotgun reads. You'd need to resort to a BAC-to-BAC method or have some super long reads, or mate pairs...
Forum: De novo discovery 01-15-2013, 07:25 AM
Replies: 9
Views: 2,038
Posted By nickloman
DH10B is known to have a large segmental...

DH10B is known to have a large segmental duplication around 113kb. This will be assembled into a single consensus contig, hence the reason for the large gap I suspect.
Forum: Sample Prep / Library Generation 01-07-2013, 02:04 AM
Replies: 10
Views: 5,955
Posted By nickloman
Not yet, although we have a manuscript in review....

Not yet, although we have a manuscript in review. I'll update the thread when there is a citation.
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