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Forum: Academic/Non-Profit Jobs 11-20-2015, 07:25 AM
Replies: 0
Views: 630
Posted By The_Roads
Research Associate in Genomics Core Facility - Miami

We have an opening for an Research Associate in the Oncogenomics Core Facility in the Sylvester Comprehensive Cancer Center at the University of Miami (Position #P00007534). We are an expanding...
Forum: Core Facilities 10-15-2015, 09:09 PM
Replies: 6
Views: 1,991
Posted By The_Roads
Thank you Brian, that makes sense.

Thank you Brian, that makes sense.
Forum: Core Facilities 10-14-2015, 08:53 AM
Replies: 6
Views: 1,991
Posted By The_Roads
Targeted amplicon sequencing, is full overlap necessary?

Hi,

Has anyone got experience running targeted amplicon libraries at less than full overlap?

We have been asked to run thunderbolts libraries that recommend 2x 250 bp to achieve full overlap...
Forum: Core Facilities 03-18-2014, 08:44 AM
Replies: 2
Views: 3,493
Posted By The_Roads
Thanks. We wont be using it for LIMS, we are...

Thanks. We wont be using it for LIMS, we are interested in using it to track the progress of jobs, and auditing and managing billing.

We are a small core but we are about to embark on an expansion...
Forum: Core Facilities 03-17-2014, 09:22 AM
Replies: 2
Views: 3,493
Posted By The_Roads
iLab for genomics core

Hi,

Does anyone have any experience, comments or general opinion on the value or usability of iLab core facility management software?

cheers,
The_Roads
Forum: Genomic Resequencing 09-20-2012, 05:59 AM
Replies: 11
Views: 6,930
Posted By The_Roads
standard Sigma pcr cleanup columns and...

standard Sigma pcr cleanup columns and Clontech/Macherey-Nagel nucleospin columns have both worked fine for us to supply template to our core. i am pretty certain they do not do any further clean up...
Forum: Bioinformatics 09-10-2012, 06:28 AM
Replies: 6
Views: 2,342
Posted By The_Roads
yes i would agree with the above post --and...

yes i would agree with the above post --and modify my previous post. we do seem to see a lot of chimeric reads and i expect most of them are chimeras from library prep. we see very variable...
Forum: General 08-17-2012, 09:18 AM
Replies: 0
Views: 1,171
Posted By The_Roads
chimeric reads from TruSeq library prep

Hi,

We have a bunch of assemblies where we have identified chimeric reads, some of which we have verified as genuine recombination and some of which we suspect are artifact from PCR jumping during...
Forum: Ion Torrent 07-12-2012, 08:09 AM
Replies: 0
Views: 1,048
Posted By The_Roads
dealing with homopolymer/low complexity errors

Hi,

i am looking through our first pgm run sequencing long pcr fragments and assembling against a ref seq.

we have previously done the same thing on hiseqs with no issues.

for the pgm data...
Forum: Bioinformatics 06-21-2012, 01:42 PM
Replies: 2
Views: 1,312
Posted By The_Roads
CLC Genomics Machine -- anyone willing to share experiences

Hi,

Are there any CLC Genomics Machine users will to share there experiences?

Everyone loves benchmarks but i guess i am more interested in how does the system work in shared environment with...
Forum: General 06-21-2012, 01:33 PM
Replies: 14
Views: 3,995
Posted By The_Roads
i would say most talk of the error rates of ngs...

i would say most talk of the error rates of ngs grossly overemphasize the problem. yes there is a conflict rate of >>1% when you compare plain read sequences but as soon as you introduce any sort of...
Forum: Bioinformatics 03-27-2012, 03:34 PM
Replies: 6
Views: 2,342
Posted By The_Roads
i think illumina have done a pretty good job of...

i think illumina have done a pretty good job of reducing mix up of paired ends. i dont think we ever see any evidence of it. i would not expect any sequencing errors to be around 2-3% of reads.

we...
Forum: Bioinformatics 03-27-2012, 07:30 AM
Replies: 6
Views: 2,342
Posted By The_Roads
what about the other reads in the same regions?...

what about the other reads in the same regions? are they mapped specifically or do they have alternative locations?

what is library? if its pcr derived that may be an issue.
Forum: RNA Sequencing 10-08-2011, 07:02 PM
Replies: 9
Views: 2,005
Posted By The_Roads
There is a nice paper in plos1 from Helicos that...

There is a nice paper in plos1 from Helicos that looks at rRNA and mitochondrial RNA content in different preps. polyA from brain reached 45% but most were around 10%
Forum: Illumina/Solexa 01-20-2011, 07:57 AM
Replies: 2
Views: 3,494
Posted By The_Roads
reagrding this nextera purchase anyone heard...

reagrding this nextera purchase anyone heard anything about illuminas plans or targets for multiplexing? i heard the nextera purchase would allow them to increase capacity of capture/mulitplex...
Forum: General 06-07-2010, 11:10 AM
Replies: 7
Views: 2,533
Posted By The_Roads
Hi Avinash, where are your sanger primers in...

Hi Avinash,

where are your sanger primers in relation to the exon and the indel? it may be that both results are true and that you are assembling psedogene sequence that is not amplifying with...
Forum: Bioinformatics 03-29-2010, 12:15 PM
Replies: 9
Views: 4,527
Posted By The_Roads
Hi PPARG, Thanks for the reply. The internal...

Hi PPARG,

Thanks for the reply. The internal priming i mentioned was meant as internal priming during sequencing, it was something that was suggested by an illumina tech when we were discussing...
Forum: Bioinformatics 03-27-2010, 05:04 PM
Replies: 9
Views: 4,527
Posted By The_Roads
Hi, If i understand your description we have...

Hi,

If i understand your description we have seen the same thing in paired end dna sequencing.

We see a small percentage of pairs where the two reads are either on top of each other or have...
Forum: Bioinformatics 12-10-2009, 09:16 AM
Replies: 65
Views: 29,365
Posted By The_Roads
Conflicts and SNPs are not really the same thing....

Conflicts and SNPs are not really the same thing. In CLC a conflict is any variation from the ref seq or consensus. A SNP is a conflict that has passed quality and position requirements.
The...
Forum: Bioinformatics 12-10-2009, 08:12 AM
Replies: 65
Views: 29,365
Posted By The_Roads
Hi Johnny, I assume you are using CLCGWB. if so...

Hi Johnny, I assume you are using CLCGWB. if so the conflict table is not the place to look. you should run a snp detection. if you have an annotated ref seq then the table will present you with all...
Forum: Bioinformatics 12-09-2009, 09:32 AM
Replies: 2
Views: 3,599
Posted By The_Roads
IPAR recycling

Does anyone have any experience or pointers for recycling IPAR servers into assembly workstations/server?
Forum: Bioinformatics 12-09-2009, 09:28 AM
Replies: 7
Views: 2,559
Posted By The_Roads
I'd agree, as much ram as you can afford and i'd...

I'd agree, as much ram as you can afford and i'd say multicore as well. if you are going to be using two NGS platforms it sounds like you anticipate lots of throughput. if you have four or five users...
Forum: Bioinformatics 10-09-2009, 11:21 AM
Replies: 14
Views: 8,916
Posted By The_Roads
Thumbs up we've been using CLCGWB for a while now, v3.6.5...

we've been using CLCGWB for a while now, v3.6.5 is fantastic. i'd agree with the comment above, i dont think you can under estimate the benefits of putting a biologist in the driving seat with...
Forum: Bioinformatics 09-09-2009, 09:26 PM
Replies: 65
Views: 29,365
Posted By The_Roads
As an update for future readers, received some...

As an update for future readers, received some excellent help from CLC and it appears the delays we experienced were due to the way we assembled our contigs. Using conventional assembly parameters...
Forum: Bioinformatics 07-28-2009, 04:29 PM
Replies: 65
Views: 29,365
Posted By The_Roads
Hi Shawn, Thanks I'll be in touch. We...

Hi Shawn,

Thanks I'll be in touch.

We have the 64 bit version and we've already tweaked vmoptions. Everything to relating to assembling, SNP detection etc. that requires 64 bit computing is...
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