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Search: Posts Made By: ksawatzki
Forum: Bioinformatics 09-16-2019, 05:53 AM
Replies: 0
Views: 622
Posted By ksawatzki
Masurca 3.3.0 3-overlap correction errors

I've been struggling through running Masurca with PE Illumina + ONT data for a mammalian genome on a SLURM cluster for months now. I'm completely stumped by what seemed to be a straightforward...
Forum: General 12-07-2017, 12:03 PM
Replies: 1
Views: 1,879
Posted By ksawatzki
I know this is old, but I'm considering optical...

I know this is old, but I'm considering optical mapping instead of supplemental long reads. Did you ever find a core, what was the rough cost and did you ultimately find it useful?
Forum: Bioinformatics 10-24-2016, 06:28 AM
Replies: 4
Views: 1,743
Posted By ksawatzki
I don't use this program, but try putting your -o...

I don't use this program, but try putting your -o command before the input:

/home/weronika/Downloads/trim_galore_v0.4.2/trim_galore --illumina -q 20 -e 0.2 -length 43 -phred33 -o...
Forum: Bioinformatics 10-24-2016, 06:09 AM
Replies: 0
Views: 809
Posted By ksawatzki
Tool to perform alignment and consensus on specialized FASTQ dataset?

I have sequencing data that was given molecular tags, indicating they were amplified from the same molecule and should be given a value of 1. I've been searching for a sophisticated tool or set of...
Forum: Illumina/Solexa 02-23-2016, 07:28 AM
Replies: 68
Views: 24,949
Posted By ksawatzki
Yeah, I'm hoping that they'll be willing to help...

Yeah, I'm hoping that they'll be willing to help us since our paper trail involves a very early recognition of the problem, which we immediately brought to their attention. Our runs have definitely...
Forum: Illumina/Solexa 02-23-2016, 07:18 AM
Replies: 68
Views: 24,949
Posted By ksawatzki
This is a huge problem for us. We lost many...

This is a huge problem for us. We lost many thousands of dollars trying to
"fix" this problem on the library prep end, and we had tens of thousands of dollars allotted to sequencing on a government...
Forum: Sample Prep / Library Generation 06-11-2015, 05:46 AM
Replies: 3
Views: 1,241
Posted By ksawatzki
One basic thing would be to make sure all of your...

One basic thing would be to make sure all of your reagents, particularly before amplification, are RNase and DNase free, and you work in a hood treated with RNase/DNase inhibitor. If you've been...
Forum: Illumina/Solexa 06-10-2015, 07:50 AM
Replies: 68
Views: 24,949
Posted By ksawatzki
I'd contact your Illumina rep to get their...

I'd contact your Illumina rep to get their opinion. It sounds like there are regions that haven't had any trouble at all while in my area, no one I've talked to is confident or currently running the...
Forum: Illumina/Solexa 06-10-2015, 07:39 AM
Replies: 68
Views: 24,949
Posted By ksawatzki
I know that they've been working with Illumina to...

I know that they've been working with Illumina to work things out, and after contacting a few other cores in the area, it's definitely the reagent. They're an excellent core, and I'm confident that...
Forum: Illumina/Solexa 06-10-2015, 07:25 AM
Replies: 68
Views: 24,949
Posted By ksawatzki
I haven't taken a detailed look at the fastq...

I haven't taken a detailed look at the fastq since it's a complete loss for us (even though R1 is completely normal, we require both) and also because we're not involved with the sequencers...
Forum: Illumina/Solexa 06-10-2015, 06:57 AM
Replies: 68
Views: 24,949
Posted By ksawatzki
@dfhdfh I'm not sure what the range of the...

@dfhdfh
I'm not sure what the range of the problem is, but I've attached the Prinseq QC output for Read2 of one of my reagent-based failed runs. It just... immediately stops working.
Forum: Illumina/Solexa 06-08-2015, 03:06 PM
Replies: 68
Views: 24,949
Posted By ksawatzki
Great, that's very reassuring to hear. I just...

Great, that's very reassuring to hear. I just couldn't find anything that confirmed there was a known problem, the core tells me that they have it handled. Thanks!
Forum: Illumina/Solexa 06-08-2015, 12:38 PM
Replies: 68
Views: 24,949
Posted By ksawatzki
2x300 MiSeq read 2 failures due to reagent?

We have been running many libraries with a core using the PE 300 kit on their MiSeqs. We've been working with them successfully for more than a year, and I've been using a set protocol for at least a...
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