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Forum: Illumina/Solexa 03-07-2018, 10:24 PM
Replies: 3
Views: 1,308
Posted By snetmcom
the fastest sequencing time for an average run is...

the fastest sequencing time for an average run is probably Oxford Nanopore or Ion Torrent. Both of those systems do not use optical detection or enzymatic steps to build the sequences. I suppose...
Forum: Sample Prep / Library Generation 01-18-2018, 12:21 PM
Replies: 14
Views: 7,032
Posted By snetmcom
This does work, but the beads will inhibit some...

This does work, but the beads will inhibit some reactions.
Forum: Ion Torrent 01-18-2018, 12:14 PM
Replies: 5
Views: 2,294
Posted By snetmcom
The other option is to use Ion Torrent's...

The other option is to use Ion Torrent's microbial pipeline. I have not used it, but I know a group that exclusively uses it for their metagenomic workflow.
Forum: Ion Torrent 12-11-2017, 09:26 AM
Replies: 8
Views: 2,254
Posted By snetmcom
The Ampliseq RNA panels just use tmap and the...

The Ampliseq RNA panels just use tmap and the torrent suite coverage analysis tools. I don't think these libraries should be analyzed as RNAseq data as they are specifically targeted for exons.
Forum: Ion Torrent 06-11-2017, 01:06 AM
Replies: 1
Views: 1,698
Posted By snetmcom
run the Coverage Analysis Plugin that is included...

run the Coverage Analysis Plugin that is included in Torrent Suite.
Forum: Ion Torrent 01-27-2017, 09:11 AM
Replies: 4
Views: 2,310
Posted By snetmcom
ext3 is the recommended format in their...

ext3 is the recommended format in their documentation.
Forum: Ion Torrent 11-30-2016, 06:33 PM
Replies: 9
Views: 4,665
Posted By snetmcom
bad run with low quality - this looks like not...

bad run with low quality - this looks like not enough library into the template prep reaction. The test fragments are very high which means you did not have many library ISP's during loading.

I...
Forum: Pacific Biosciences 10-31-2016, 07:18 AM
Replies: 21
Views: 5,583
Posted By snetmcom
seems like there is a surprising amount of...

seems like there is a surprising amount of misinformation. Thanks for clarifying.
Forum: Ion Torrent 06-23-2016, 08:21 PM
Replies: 2
Views: 3,659
Posted By snetmcom
This is in the public datasets on ion torrent's...

This is in the public datasets on ion torrent's community webpage.
Forum: Ion Torrent 10-15-2014, 04:48 PM
Replies: 10
Views: 9,197
Posted By snetmcom
Only the torrent suite can analyze a .dat file. ...

Only the torrent suite can analyze a .dat file. The dat file is completely raw data. there is no sequence information until it is processed by the Torrent Server.
Forum: Ion Torrent 10-07-2014, 05:53 PM
Replies: 121
Views: 100,846
Posted By snetmcom
20GB seems unlikely given the throughput of the...

20GB seems unlikely given the throughput of the P1 is almost there. Read number might be more interesting.

Qiagen has gone silent, but they went on an acquisition spree getting things lined up. ...
Forum: Ion Torrent 09-10-2014, 01:20 PM
Replies: 5
Views: 1,270
Posted By snetmcom
The 50AQ17 metric of the TF's, not the run...

The 50AQ17 metric of the TF's, not the run metrics.
Forum: Ion Torrent 09-08-2014, 05:32 PM
Replies: 5
Views: 1,270
Posted By snetmcom
What's the 50aq17, and was there a data issue? ...

What's the 50aq17, and was there a data issue?
Sometimes the TF's get old, but the run is completely fine.
Forum: Ion Torrent 08-10-2014, 03:12 PM
Replies: 4
Views: 2,065
Posted By snetmcom
All of the above. It this a library you have...

All of the above. It this a library you have sequenced well before, or is it a completely new experiment.
Forum: Illumina/Solexa 07-18-2014, 06:07 PM
Replies: 3
Views: 2,063
Posted By snetmcom
Bubbles are not that uncommon. It really depends...

Bubbles are not that uncommon. It really depends on the frequency. I'd be curious if you find any tips.
Forum: Illumina/Solexa 07-18-2014, 05:58 PM
Replies: 4
Views: 1,569
Posted By snetmcom
How are you quantifying your starting DNA? ...

How are you quantifying your starting DNA? Nextera is very sensitive to starting amount.
Forum: Ion Torrent 07-18-2014, 05:49 PM
Replies: 1
Views: 1,394
Posted By snetmcom
You can do whole genome sequencing of e.coli on a...

You can do whole genome sequencing of e.coli on a 316 chip, so you can easily fit several transcriptomes on a 318 chip.
Forum: Illumina/Solexa 06-08-2014, 09:54 PM
Replies: 2
Views: 3,745
Posted By snetmcom
What did you try for sonication? I agree that...

What did you try for sonication? I agree that lower input is what you should adjust for Nextera.
Forum: Illumina/Solexa 06-08-2014, 09:52 PM
Replies: 6
Views: 2,515
Posted By snetmcom
i would also vote for irfanview. It has batch...

i would also vote for irfanview. It has batch editing tools that are real handy.
Forum: The Pipeline 06-08-2014, 09:51 PM
Replies: 19
Views: 20,206
Posted By snetmcom
I'm curious about this part as well. I wonder if...

I'm curious about this part as well. I wonder if Thermo Fisher dumped any ties with Genia after the Life acquisition?
Forum: Ion Torrent 06-08-2014, 09:49 PM
Replies: 2
Views: 5,830
Posted By snetmcom
Store libraries as you would any DNA. I have...

Store libraries as you would any DNA. I have rerun libraries well over a year old from -20.
Freeze/thaw cycles will damage the DNA over time.
Forum: Ion Torrent 06-08-2014, 09:42 PM
Replies: 9
Views: 8,668
Posted By snetmcom
I agree it's not unusual to see some homopolymer...

I agree it's not unusual to see some homopolymer errors, but I do find it unusual to see it trend on only one strand. Are you aligning to the whole genome? Have you tried aligning the data with the...
Forum: Bioinformatics 06-08-2014, 09:36 PM
Replies: 4
Views: 2,745
Posted By snetmcom
You may also want to check out Ugene. It's a GUI...

You may also want to check out Ugene. It's a GUI based tool that has several alignment tools including bwa.

I have not run this on large datasets, but it has worked very well for microbial and...
Forum: Illumina/Solexa 06-02-2014, 08:18 PM
Replies: 14
Views: 4,677
Posted By snetmcom
Did you perform any library QC? Are you certain...

Did you perform any library QC? Are you certain the Ribo depletetion was a success? That could account for a surplus of duplicate reads.
Forum: Introductions 05-29-2014, 07:20 PM
Replies: 8
Views: 2,862
Posted By snetmcom
You can have the Ion platforms give you fastq. ...

You can have the Ion platforms give you fastq. They will be barcode separated unless you want to do the barcode splitting yourself.

There might be some confusion with Ion Reporter. This is...
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