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Search: Posts Made By: r.rosati
Forum: Bioinformatics 10-29-2019, 10:06 AM
Replies: 3
Views: 641
Posted By r.rosati
Hi! Yes you can BLAST it, but since it's a short...

Hi! Yes you can BLAST it, but since it's a short sequence it's best if you use the `blastn` algorithm instead of the `megablast` one. You can also decrease the word size to 7 to increase sensitivity....
Forum: Ion Torrent 10-12-2019, 04:07 PM
Replies: 1
Views: 333
Posted By r.rosati
Ciao Chiara! Ion Torrent's emulsion PCR takes...

Ciao Chiara! Ion Torrent's emulsion PCR takes place outside the sequencer. You can either perform it on the OneTouch2 device (and then purify the beads on the ES2) or automatically on the Ion Chef....
Forum: Ion Torrent 08-01-2019, 10:13 AM
Replies: 19
Views: 2,506
Posted By r.rosati
4. The chips can be cleaned and reused...

4. The chips can be cleaned and reused indefinitely if you're willing to put up with minor contamination (83% clean is what I've been told.)

Hi. Do you actually have a protocol for that? I've...
Forum: General 07-11-2019, 03:34 AM
Replies: 4
Views: 1,699
Posted By r.rosati
I'd suggest, choose a topic you're passionate...

I'd suggest, choose a topic you're passionate about (and you keep current about). Good luck!
Forum: Ion Torrent 07-09-2019, 02:04 PM
Replies: 2
Views: 911
Posted By r.rosati
Hi, you're right, the v3 version...

Hi,
you're right, the v3 version...
Forum: Ion Torrent 06-14-2019, 06:01 AM
Replies: 2
Views: 1,275
Posted By r.rosati
I work in a lab with an Ion Proton. Despite...

I work in a lab with an Ion Proton.
Despite chats that "some laboratories" were already testing it, the PII chip was never released.
What was released, for the new S5 platform, is the Ion 550 chip;...
Forum: Bioinformatics 06-04-2019, 05:34 PM
Replies: 3
Views: 505
Posted By r.rosati
Hi! Regarding your question, 2E-10 means...

Hi!
Regarding your question, 2E-10 means 2*10^-10, and 2E-20 means 2*10^-20. So 2E-20 is lower.
However these values are pretty stringent, if you have a 2E-10 hit in one database, it'd take a...
Forum: Introductions 06-04-2019, 05:28 PM
Replies: 5
Views: 1,038
Posted By r.rosati
Hi, I'm glad you could figure it out! Cheers!

Hi, I'm glad you could figure it out! Cheers!
Forum: Introductions 06-04-2019, 04:09 AM
Replies: 5
Views: 1,038
Posted By r.rosati
I'd love to help more (a fellow researcher from...

I'd love to help more (a fellow researcher from Brazil!), but one needs to fill an application form to get the software and apparently it might take up to 2 weeks for the approval? I've never seen...
Forum: Bioinformatics 06-04-2019, 03:45 AM
Replies: 3
Views: 505
Posted By r.rosati
I confess I'm not sure I fully understood your...

I confess I'm not sure I fully understood your question. Do you mean that there are certain hits that are retrieved from one database, and don't appear when searching on the other? If so, then it...
Forum: Introductions 06-01-2019, 05:49 AM
Replies: 5
Views: 1,038
Posted By r.rosati
Hi! In your screenshot, isn't "whole"...

Hi! In your screenshot, isn't "whole" selected?
Forum: Bioinformatics 05-30-2019, 07:12 PM
Replies: 4
Views: 617
Posted By r.rosati
Yes, but... if the index is just OK, he could as...

Yes, but... if the index is just OK, he could as well do
touch 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
and the message won't bother him anymore.
Forum: Bioinformatics 05-28-2019, 06:32 PM
Replies: 4
Views: 617
Posted By r.rosati
This specifically ("The index file is older than...

This specifically ("The index file is older than the data file") is a warning and not an error. If you trust the index, you can in all honesty ignore this spammy message.
Anyways, see if this thread...
Forum: Illumina/Solexa 05-27-2019, 04:51 AM
Replies: 3
Views: 1,075
Posted By r.rosati
Glad to be of help! As an afterthought - one...

Glad to be of help!
As an afterthought - one can't blame the software for calling both "mismatches". Not the sequencer, nor the software know the "truth" and they don't know if a base is a...
Forum: Illumina/Solexa 05-27-2019, 03:24 AM
Replies: 3
Views: 1,075
Posted By r.rosati
The confusion comes from the use of "mismatch"...

The confusion comes from the use of "mismatch" both for "sequencing error" and "difference between barcodes".
If you allow one sequencing error, then the number of differences between barcodes...
Forum: Ion Torrent 05-24-2019, 01:43 PM
Replies: 1
Views: 1,334
Posted By r.rosati
I really thought this thread would get more...

I really thought this thread would get more traction.
Forum: Sample Prep / Library Generation 05-14-2019, 06:21 PM
Replies: 6
Views: 1,014
Posted By r.rosati
I'm sorry, did I misunderstand you? I thought you...

I'm sorry, did I misunderstand you? I thought you were considering libraries, and then what I meant is that qPCR with adaptor-specific primers is a better option than equalizing with SPRI beads. The...
Forum: Sample Prep / Library Generation 05-13-2019, 02:47 PM
Replies: 6
Views: 1,014
Posted By r.rosati
This is basically the idea behind ThermoFisher's...

This is basically the idea behind ThermoFisher's "Equaliser" NGS kit. In our hands it didn't work particularly well, though. PCR is really more accurate.
Forum: Ion Torrent 04-25-2019, 03:07 PM
Replies: 1
Views: 1,334
Posted By r.rosati
Substantial change in TS VariantCaller default parameters

Hi all,
please be aware that Thermo did some very substantial changes in the default VariantCaller parameters for germline exomes in TS version 5.10. For example, the default "Germline low...
Forum: Events / Conferences 02-02-2019, 04:58 AM
Replies: 1
Views: 1,206
Posted By r.rosati
CORRECTION: 601 points are needed this year to...

CORRECTION: 601 points are needed this year to reach the finals.
Forum: General 02-01-2019, 04:58 PM
Replies: 2
Views: 1,233
Posted By r.rosati
Hi! Although nothing happens on the surface, if...

Hi! Although nothing happens on the surface, if you launch IGV via command line, you should see some error messages on the terminal. This might lead you to some information about the issue.
Forum: Events / Conferences 01-31-2019, 11:54 AM
Replies: 1
Views: 1,206
Posted By r.rosati
Bioinformatics Contest 2019 on Stepik

Hello all,
the people at St. Petersburg's Bioinformatics Institute​​​ (https://bioinf.me/en) are organizing their annual Bioinformatics Contest​ (https://bioinf.me/en/contest). It's an enjoyable...
Forum: Bioinformatics 09-06-2018, 08:56 AM
Replies: 2
Views: 828
Posted By r.rosati
Hi! RepeatMasker identifies interspersed repeats...

Hi! RepeatMasker identifies interspersed repeats by comparing it with predefined sequence libraries. Your species might just have different repeats from the tables that RepearMasker uses. At the same...
Forum: Ion Torrent 07-19-2018, 02:24 PM
Replies: 4
Views: 4,794
Posted By r.rosati
Hi, by their size, they do look like dimers....

Hi,
by their size, they do look like dimers. How are the primers like? In the end, the first step is just a PCR - if you get dimers, you won't get much product (if any) and the rest of the...
Forum: Ion Torrent 07-12-2018, 11:56 AM
Replies: 9
Views: 6,593
Posted By r.rosati
PS - in our S5, the VM has access to 12 cores. VM...

PS - in our S5, the VM has access to 12 cores. VM memory is indeed 40 GB.
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