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Search: Posts Made By: jkersh
Forum: Core Facilities 04-20-2015, 08:02 AM
Replies: 1
Views: 2,507
Posted By jkersh
Looking for opinions on stopping HiSeq 2000 service contract

Hello everyone,

We currently have an older HiSeq 2000 housed in our facility (V3 runs only) that isn't currently getting much use because of the low cost of V4 runs. We are considering taking it...
Forum: Bioinformatics 12-14-2011, 07:27 AM
Replies: 3
Views: 1,453
Posted By jkersh
I have just run into the same problem, has anyone...

I have just run into the same problem, has anyone found a way to work around the sort by name issue in Samtools? Or is there another way to do this?
Forum: Bioinformatics 09-14-2011, 02:40 PM
Replies: 2
Views: 980
Posted By jkersh
PEMer with Illumina?

Has anyone run the PEMer workflow using Illumina data? I have been looking through the documentation and have created the conversion file from the Maq output, but there doesn't seem to be much...
Forum: Bioinformatics 03-01-2011, 10:12 AM
Replies: 0
Views: 901
Posted By jkersh
Bfast match abort error

I have just started playing around with Bfast for single-end alignment of E. coli mutants to a reference genome. I got through all of the steps in making the reference and making the index files...
Forum: Illumina/Solexa 10-01-2010, 10:07 AM
Replies: 16
Views: 4,586
Posted By jkersh
Hi Harold, We recently got data from several...

Hi Harold,
We recently got data from several multiplexed 36bp single-read E. coli samples and are starting to analyze them (we couldn't find anyone to run paired-end lanes with us at the time). I...
Forum: Illumina/Solexa 05-20-2010, 07:59 AM
Replies: 16
Views: 4,586
Posted By jkersh
I agree that SOLiD would be better for this, but...

I agree that SOLiD would be better for this, but we only have an Illumina system available to us. We think the most likely mutations with be SNPs, but it is likely we will also find a variety of...
Forum: Illumina/Solexa 05-20-2010, 07:47 AM
Replies: 16
Views: 4,586
Posted By jkersh
Please ignore the barcoding question relating to...

Please ignore the barcoding question relating to paired-end reads, just realized I was thinking about incorrectly!
Forum: Illumina/Solexa 05-18-2010, 03:41 PM
Replies: 16
Views: 4,586
Posted By jkersh
Thanks for all of the information, it is hard to...

Thanks for all of the information, it is hard to find everything in one place!

Our plan is to run paired-end with 36 cycles to catch genomic rearrangements as well as SNPs. I am thinking of...
Forum: Illumina/Solexa 05-05-2010, 12:28 PM
Replies: 16
Views: 4,586
Posted By jkersh
I am still waiting to find out pricing for single...

I am still waiting to find out pricing for single end versus paired end runs with multiplexing, but I am trying to figure out if I should be using one versus the other for any specific reason other...
Forum: Illumina/Solexa 05-04-2010, 01:05 PM
Replies: 16
Views: 4,586
Posted By jkersh
Illumina for resequencing E. coli

Hi, I just started a project where we need to resequence many E. coli mutants using an Illumina GAII system. Anyone have any thoughts on paired-end versus single end, potentially with multiplexing...
Forum: General 05-04-2010, 12:34 PM
Replies: 1
Views: 1,259
Posted By jkersh
Newbie questions on computers and programs

Hi, I have just started a project that involves resequencing E. coli strains to identify SNPs and have no idea where to go for information. We have access to an Illumina GA system but have no idea...
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