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Search: Posts Made By: r.rosati
Forum: Ion Torrent 04-19-2018, 07:40 AM
Replies: 3
Views: 252
Posted By r.rosati
Thank you!

Thank you!
Forum: Ion Torrent 04-19-2018, 05:02 AM
Replies: 3
Views: 252
Posted By r.rosati
Hi, I can't help directly but I'd suggest you...

Hi, I can't help directly but I'd suggest you contact the administrator (galaxy.contact {a-t} curie.fr (https://galaxy-public.curie.fr/static/mentions_legales.txt)) and ask if they could share their...
Forum: Ion Torrent 04-16-2018, 08:10 AM
Replies: 1
Views: 282
Posted By r.rosati
I only have part of what you're looking for,...

I only have part of what you're looking for, namely, well dimensions; and unfortunately it doesn't cover the PII. However, here it is:
https://onlinelibrary.wiley.com/doi/pdf/10.1002/elps.201200424...
Forum: Illumina/Solexa 04-16-2018, 07:30 AM
Replies: 2
Views: 299
Posted By r.rosati
This patent record is a nice read regarding the...

This patent record is a nice read regarding the FuPa reagent:
https://patents.google.com/patent/US8728728B2/en
Forum: Bioinformatics 04-11-2018, 05:17 AM
Replies: 7
Views: 531
Posted By r.rosati
Thank you. I'm very curious to see the result of...

Thank you. I'm very curious to see the result of the survey!
Forum: Bioinformatics 04-10-2018, 12:10 PM
Replies: 7
Views: 531
Posted By r.rosati
I humbly disagree. In my opinion, the biological...

I humbly disagree. In my opinion, the biological reality is that genes encode multiple isoforms; naming an isoform as "principal" is an artificial layer which we apply to the "biological reality" to...
Forum: Bioinformatics 04-10-2018, 07:52 AM
Replies: 7
Views: 531
Posted By r.rosati
...Excuse me for my ignorance, but exactly, what...

...Excuse me for my ignorance, but exactly, what is the issue they're trying to address by deciding to implement a clinically-driven primary transcript?
Forum: Ion Torrent 02-26-2018, 05:52 AM
Replies: 1
Views: 831
Posted By r.rosati
Hi! There are three run reports publicly(*)...

Hi!
There are three run reports publicly(*) available for the 540 chip here:
https://apps.thermofisher.com/apps/publiclib/#/datasets

The "download" refers to just the PDF reports, but if you...
Forum: Ion Torrent 01-24-2018, 12:32 PM
Replies: 1
Views: 893
Posted By r.rosati
Ion Torrent sequencers comparison

Hello,
so, now Thermo has 8 Ion Torrent models (https://www.thermofisher.com/search/browse/category/us/en/602565?navId=10972%2B4294959573) for sale (for future reference: PGM, PGM-Dx, Proton, S5, S5...
Forum: Bioinformatics 11-29-2017, 03:56 AM
Replies: 2
Views: 431
Posted By r.rosati
I'm not experienced, but since nobody replied...

I'm not experienced, but since nobody replied yet: if in `makeblastdb` you chose to name the database "nt", then in `blastn` have you tried using this name, i.e. `-db nt` instead of the complete...
Forum: Ion Torrent 11-16-2017, 03:36 AM
Replies: 6
Views: 908
Posted By r.rosati
I see. Getting them right would take some...

I see. Getting them right would take some experimenting.
Forum: Ion Torrent 11-14-2017, 08:41 AM
Replies: 6
Views: 908
Posted By r.rosati
...I gave you a very unorthodox answer, didn't I?...

...I gave you a very unorthodox answer, didn't I? If you're working with diagnostics, I understand that you can't alter the chips. I'm afraid I don't have a solution then.
If you work on research...
Forum: Ion Torrent 11-14-2017, 08:23 AM
Replies: 6
Views: 908
Posted By r.rosati
What I mean is that the chips are apparently...

What I mean is that the chips are apparently labeled in batch. If you can attach a sticker with the right information on it, and I mean information taken from a real 318 chip (not the one image...
Forum: Ion Torrent 11-14-2017, 08:06 AM
Replies: 6
Views: 908
Posted By r.rosati
Hi, the information on the chip barcode is...

Hi,
the information on the chip barcode is nothing much; lot number and chip type, I think. Why do you say that adding a sticker is not an option?
[Edit: it appears that the barcodes are individual]
Forum: Genomic Resequencing 09-13-2017, 06:09 AM
Replies: 4
Views: 1,951
Posted By r.rosati
In my humble opinion I would think that this...

In my humble opinion I would think that this would improve dramatically the chance to find the translocation algorithmically (as opposed as curating the data manually). Still, if the breakpoint is...
Forum: Genomic Resequencing 09-12-2017, 05:49 AM
Replies: 4
Views: 1,951
Posted By r.rosati
My two cents ... "It depends". If it's an...

My two cents ... "It depends".
If it's an unbalanced translocation, in a condition where this is the sole genomic imbalance, then your best bet would actually not be NGS but microarray CGH, which...
Forum: Bioinformatics 09-11-2017, 12:30 PM
Replies: 4
Views: 489
Posted By r.rosati
Does this help? ...

Does this help?

https://gatkforums.broadinstitute.org/gatk/discussion/7571/errors-in-sam-bam-files-can-be-diagnosed-with-validatesamfile
Forum: Ion Torrent 09-11-2017, 06:48 AM
Replies: 0
Views: 808
Posted By r.rosati
Where the short BAMs are

This is not a question, but a tip. It might be common knowledge, but well, if you're a bit on your own as we are, you might not know this (our Institute's bioinformatician found this info when she...
Forum: Introductions 05-29-2017, 11:11 AM
Replies: 2
Views: 670
Posted By r.rosati
Welcome Vimac! Leuven is such a beutiful city,...

Welcome Vimac! Leuven is such a beutiful city, and what an amazing university KULeuven is!
Forum: Bioinformatics 05-18-2017, 04:51 PM
Replies: 12
Views: 1,045
Posted By r.rosati
You might find some traction for your question on...

You might find some traction for your question on reddit.com/r/labrats , it's a pretty nice subreddit. Not everybody will agree with you, but that's just average.
Forum: Bioinformatics 05-03-2017, 11:28 AM
Replies: 20
Views: 7,372
Posted By r.rosati
A post of mine from two days ago got stuck in...

A post of mine from two days ago got stuck in moderation limbo; it's a pity because it had some good links.
I was commenting that this thread is pretty interesting.
The sequence you mention is an...
Forum: Bioinformatics 04-29-2017, 11:40 AM
Replies: 2
Views: 607
Posted By r.rosati
This is the full sequence of a matching protein...

This is the full sequence of a matching protein that you're seeing.
Your sequence translates to (http://www.bioinformatics.org/sms2/translate.html):...
Forum: Bioinformatics 04-27-2017, 11:18 AM
Replies: 20
Views: 7,372
Posted By r.rosati
...on the good side I should specify that we own...

...on the good side I should specify that we own an Ion Proton, so over the time I actually became very good at finding out why a variant call went wrong.
Forum: Bioinformatics 04-26-2017, 09:46 AM
Replies: 20
Views: 7,372
Posted By r.rosati
I'm definitely not the most knowledgeable around...

I'm definitely not the most knowledgeable around here, but if you would like to provide an example, we could work it out - i.e. an IGV screenshot, using the GRCh38 reference, of a BAM file showing...
Forum: Bioinformatics 04-26-2017, 06:45 AM
Replies: 20
Views: 7,372
Posted By r.rosati
Well, specifically on this issue, on one side I...

Well, specifically on this issue, on one side I would say that 99.99% of the times (not always) this happens when a very common variation in hg19 becomes reference on GRCh38 or vice-versa.
So in a...
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