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Forum: Metagenomics 06-07-2016, 06:46 AM
Replies: 0
Views: 1,475
Posted By trexbob
auto log-off on IMG website

Wow, who thought it was a good idea to implement an auto log-off after 55 minutes...?! :mad: Over the past few days I have found myself distracted for a little while on something else and go back to...
Forum: Bioinformatics 01-06-2016, 05:43 AM
Replies: 15
Views: 4,501
Posted By trexbob
Thanks Brian, I appreciate the response! It's...

Thanks Brian, I appreciate the response! It's been my experience that merging reads has not improved the datasets with OMEGA, but has helped with Megahit (our reads have been merging 70-90%).

More...
Forum: Bioinformatics 01-05-2016, 10:44 AM
Replies: 15
Views: 4,501
Posted By trexbob
You might try normalizing your data first, using...

You might try normalizing your data first, using bbnorm. It helped me tremendously. Like rhinoceros above, I've found MEGAHIT not as good as some others. I suggest you might try OMEGA. Also some...
Forum: Academic/Non-Profit Jobs 03-13-2014, 04:54 AM
Replies: 0
Views: 1,026
Posted By trexbob
Fellow position MS or PhD post-doc level at CDC Tobacco Lab

http://www.careerbuilder.com/JobSeeker/Jobs/JobDetails.aspx?sc_cmp1=js_jrp_jobclick&APath=2.21.0.0.0&job_did=JHQ7F96M002XVN4BWT7&showNewJDP=yes&IPath=QHKV0A

Notes: This is an ORISE Fellow...
Forum: Illumina/Solexa 02-04-2014, 04:45 AM
Replies: 10
Views: 6,245
Posted By trexbob
This depends on the genus/species and how diverse...

This depends on the genus/species and how diverse they are in the region that is being looked at. Data analysis parameters figure in as well. The higher % ID you pick OTUs at, the more species will...
Forum: Introductions 02-03-2014, 04:26 AM
Replies: 2
Views: 1,791
Posted By trexbob
Welcome Robin! Nice tool you've developed...

Welcome Robin! Nice tool you've developed there...
Forum: Ion Torrent 11-25-2013, 06:02 AM
Replies: 2
Views: 3,413
Posted By trexbob
Hi Sergio, I'm also relatively new at this...

Hi Sergio,
I'm also relatively new at this also, but... I can help somewhat. The Ion Torrent software usually trims off the 5' adapter, so unless you have a primer, you generally don't have to do 5'...
Forum: Bioinformatics 11-19-2013, 04:16 AM
Replies: 7
Views: 2,949
Posted By trexbob
I'll throw my 2 cents in... from recent...

I'll throw my 2 cents in... from recent experience. Less cores might be slower but not enough RAM can really ruin your day. More RAM is better than faster RAM, if you're on a budget.
Forum: Metagenomics 11-13-2013, 04:11 AM
Replies: 5
Views: 3,887
Posted By trexbob
I started off using the binary, but as I...

I started off using the binary, but as I mentioned, it seems like it's looking for paired data exclusively, so I switched to using 1.3 (non-binary) version. I am still having trouble getting the...
Forum: Metagenomics 11-12-2013, 08:13 AM
Replies: 5
Views: 3,887
Posted By trexbob
I'm using single reads, so the -m is for...

I'm using single reads, so the -m is for specifying mate-paired reads, and the -i parameter is for insert size - I can't give an insert size as that only applies to paired reads... right?

I...
Forum: Metagenomics 10-31-2013, 04:19 AM
Replies: 5
Views: 3,887
Posted By trexbob
Metamos help request

Has anyone out there used MetAmos with a single read fastq file? I've downloaded the binary with Blast DBs and tried using initPipeline -q -1 myfile.fastq which seems to work, but then when I do...
Forum: Metagenomics 10-24-2013, 05:31 AM
Replies: 1
Views: 3,543
Posted By trexbob
What platform are you sequencing on? I would...

What platform are you sequencing on? I would like to see other's responses to this... I am sequencing on Ion Torrent PGM and the difference between 94, 97 and 99% is significant. I believe even...
Forum: Bioinformatics 10-24-2013, 05:13 AM
Replies: 7
Views: 3,724
Posted By trexbob
Hi I can try to help... but you'll get better...

Hi I can try to help... but you'll get better answers on the QIIME google web group.
Like rhinoceros says, you should really go over the tutorials, they answer a lot of questions a new person might...
Forum: Sample Prep / Library Generation 09-24-2013, 06:47 AM
Replies: 5
Views: 2,848
Posted By trexbob
I've had good luck with NEB's Q5 Hot Start Hi Fi...

I've had good luck with NEB's Q5 Hot Start Hi Fi 2x Master mix. My negative control PCR's are always negative. Are you using filtered pipet tips and quality molecular biology grade water?
Forum: General 09-17-2013, 04:56 AM
Replies: 3
Views: 2,789
Posted By trexbob
I've been using the 515F-806R recently with...

I've been using the 515F-806R recently with adapters and barcodes on the primers. I have had a few samples not work, but I think it's more a problem with the DNA extraction for those particular...
Forum: Bioinformatics 09-09-2013, 05:08 AM
Replies: 2
Views: 1,881
Posted By trexbob
Hi Katie, Were the five that failed somehow...

Hi Katie,
Were the five that failed somehow different from the others as far as what they were from? Is there a possibility that those five somehow had a chemical present in the isolated DNA that...
Forum: Introductions 03-27-2013, 10:35 AM
Replies: 0
Views: 930
Posted By trexbob
Introduction

Hi, I'm relatively new to the NGS world, I'm a microbiologist at CDC in Atlanta. Working on doing some 16s microbial community analyses of soil/plant matter. Looking forward to learning a lot here.
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