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Search: Posts Made By: r.rosati
Forum: Bioinformatics 11-29-2017, 04:56 AM
Replies: 2
Views: 369
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, 04:36 AM
Replies: 6
Views: 533
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, 09:41 AM
Replies: 6
Views: 533
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, 09:23 AM
Replies: 6
Views: 533
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, 09:06 AM
Replies: 6
Views: 533
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, 07:09 AM
Replies: 4
Views: 1,560
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, 06:49 AM
Replies: 4
Views: 1,560
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, 01:30 PM
Replies: 4
Views: 399
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, 07:48 AM
Replies: 0
Views: 483
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, 12:11 PM
Replies: 2
Views: 613
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, 05:51 PM
Replies: 12
Views: 869
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, 12:28 PM
Replies: 20
Views: 4,468
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, 12:40 PM
Replies: 2
Views: 543
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, 12:18 PM
Replies: 20
Views: 4,468
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, 10:46 AM
Replies: 20
Views: 4,468
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, 07:45 AM
Replies: 20
Views: 4,468
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...
Forum: Bioinformatics 04-20-2017, 09:01 AM
Replies: 20
Views: 4,468
Posted By r.rosati
About rs4940595: you're right, the hg19 build...

About rs4940595: you're right, the hg19 build includes the (more frequent) T allele, that codes for a stop codon; while GRCh38 includes the less frequent G allele. Anyways, considering that the two...
Forum: Ion Torrent 04-20-2017, 08:21 AM
Replies: 2
Views: 1,053
Posted By r.rosati
Thanks! I think I'll go with buying dodecyl...

Thanks! I think I'll go with buying dodecyl benzene sulfonic acid (DBSA) and undecane, they're both relatively cheap; and prepare the 5% DBSA in undecane solution.
Forum: Ion Torrent 04-18-2017, 10:28 AM
Replies: 2
Views: 1,053
Posted By r.rosati
Chip Preparation Solution recipe?

Hello,
we have several Ion PI v2 chips, and we're successfully using them with Hi-Q chemistry kits. However, we're running short of Chip Preparation Solution, and Thermo has discontinued it. I know...
Forum: Bioinformatics 04-13-2017, 12:33 PM
Replies: 10
Views: 1,554
Posted By r.rosati
...Any news?

...Any news?
Forum: Bioinformatics 04-04-2017, 01:25 PM
Replies: 10
Views: 1,554
Posted By r.rosati
I have half an hypothesis. See if you agree. By...

I have half an hypothesis. See if you agree.
By the (blurry) coordinates it seems like you're using hg19, is this correct? If so, then ACTB is within the window chr7:5,566,700-5,570,300. I'll use...
Forum: Bioinformatics 03-31-2017, 05:23 PM
Replies: 10
Views: 1,554
Posted By r.rosati
Curious... can you provide a screenshot?

Curious... can you provide a screenshot?
Forum: Bioinformatics 03-31-2017, 01:28 PM
Replies: 10
Views: 1,554
Posted By r.rosati
I agree with Bukowski, if you're visualizing the...

I agree with Bukowski, if you're visualizing the data against hg19, try switching to GRCh38 - or vice-versa. Your collaborator aligned the data against a genome build that's different from the one...
Forum: Bioinformatics 02-09-2017, 11:12 AM
Replies: 587
Views: 105,014
Posted By r.rosati
Thank you... Indeed I ran it on a ssh session...

Thank you... Indeed I ran it on a ssh session from a computer that had pt_BR as LC_NUMERIC.

I've read Zhou's comment (http://seqanswers.com/forums/showpost.php?p=204050&postcount=15) on indels and...
Forum: Bioinformatics 02-08-2017, 11:14 AM
Replies: 587
Views: 105,014
Posted By r.rosati
BBmap on Ion data

Hello,
I tried to run BBmap to call variants on four BAM files (2 parents, 2 children) generated from exome sequencing on an Ion Proton machine (TMAP software).

The bbmap command was:...
Showing results 1 to 25 of 43

 


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