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Forum: Ion Torrent 01-27-2017, 10:12 AM
Replies: 4
Views: 3,172
Posted By aguffanti
Well, format the disk in ext3, follow the...

Well, format the disk in ext3, follow the instructions to mount it in the tsvm and .. good luck ! It's absolutely impossible and even the support does not know it .. Then, before throwing the disk...
Forum: Ion Torrent 01-26-2017, 08:25 AM
Replies: 4
Views: 3,172
Posted By aguffanti
Tank you Kevin - I actually fund the way....

Tank you Kevin - I actually fund the way. Important thing, it must be a NTFS formatted disk, otherwise the S5 will not read it, regardless of all your efforts !

Regards,

Alessandro
Forum: Ion Torrent 12-13-2016, 09:40 AM
Replies: 4
Views: 3,172
Posted By aguffanti
Adding an external USB disk to S5

Dear colleagues: did any of you have any luck in connecting a Linux-formatted external USB disk to Ion S5 and make it visible to the Torrent Server Virtual Machine (and hence to the Torrent Browser...
Forum: Bioinformatics 09-12-2013, 06:46 AM
Replies: 46
Views: 20,170
Posted By aguffanti
Cuffllinks variance, gene expression level and ifferential expression

Hello ! which kind of sequencing was that - fragment or paired ends ? it changes a lot

You have to look at the *count.tracking files and examine the count variance values

There are instances...
Forum: Ion Torrent 03-02-2013, 02:02 AM
Replies: 27
Views: 19,257
Posted By aguffanti
Thanks for the links, this is what I was looking...

Thanks for the links, this is what I was looking for !

I will also experiment with the Ion Torrent Virtualized software

Yes the Mosaik Aligner output I sent was from a failed run (incomplete...
Forum: Ion Torrent 03-01-2013, 11:41 AM
Replies: 27
Views: 19,257
Posted By aguffanti
Re: assembly

Hi - as I said, I don't own a PGM, I am just experimenting in silico ;-)

However I finally suceeded in aligning at least the DH10B dataset to its genome with Mosaik - all the others seem to have...
Forum: Ion Torrent 03-01-2013, 08:24 AM
Replies: 27
Views: 19,257
Posted By aguffanti
Re:

Hi - I don't own the machine, so how do I get hold of TMAP ?

I am trying to evaluate the quality of the data BEFORE considering a purchase

Keep in touch

Alessandro
Forum: Ion Torrent 03-01-2013, 07:51 AM
Replies: 27
Views: 19,257
Posted By aguffanti
Smile Referenced assembly with Ion Torrent - Mosaik from fastq files

Hi - has anybody tried referenced or de novo assembly from the .sam (or .fastq) files and ion Torrent datasets ? I downloaded the following data sets from the ion Community:

B7-143
B7-295...
Forum: SOLiD 12-16-2011, 05:39 AM
Replies: 5
Views: 2,758
Posted By aguffanti
I made a number of Whole Transcriptome Analyses...

I made a number of Whole Transcriptome Analyses with SOLiD 50bp fragments and fusion detection with Lifescope WTA pipeline. It does work quite well, although I would agree that there will be false...
Forum: SOLiD 08-10-2011, 05:50 AM
Replies: 26
Views: 14,706
Posted By aguffanti
Reecent comparison of SOLiD aligners

Next generation sequencing has lower sequence coverage and poorer
SNP-detection capability in the regulatory regions

Weixin Wang, Zhi Wei, Tak-Wah Lam & Junwen Wang

Nature SCIENTIFIC REPORTS |...
Forum: SOLiD 01-29-2011, 06:12 AM
Replies: 2
Views: 2,293
Posted By aguffanti
Me too..

Hi! I made 12 full exomes and I just recently discovered that diBayes, for whatever reason, tends to call too few aligned reads even where there is noce read coverage. As a consequence, SNPs may be...
Forum: SOLiD 08-18-2010, 08:20 AM
Replies: 19
Views: 5,817
Posted By aguffanti
SAGE HSsreference genome format

Hi. You need the Genome reference sequence from NCBI. Check that the
chromosome headers have this format:

>gi|224384759|gb|CM000672.1| Homo sapiens chromosome 10, GRC primary reference assembly
...
Forum: SOLiD 07-19-2010, 12:40 PM
Replies: 2
Views: 2,415
Posted By aguffanti
Jing, there is a command line version which you...

Jing, there is a command line version which you can get from support. Also did you check the rwx permissions on the filesystem you are using ? if you can not write on the disk the buttons will be...
Forum: SOLiD 07-19-2010, 12:25 PM
Replies: 19
Views: 5,817
Posted By aguffanti
It's dangerous to count tags only once randomly....

It's dangerous to count tags only once randomly. I postprocess the results.tab file and associate the refseq ID from a mySQL table which lnks genbank ID with RefSeq. Single RefSeqs may have many tags...
Forum: SOLiD 07-19-2010, 12:22 PM
Replies: 2
Views: 2,705
Posted By aguffanti
miRNA mapping

Hi - I would use SHRiMP from M.Brudno's group to map SOLiD reads against miRNA db. It is slow but it does contain a 'miRNA' specific mode

Kind regards,

Alessandro
Forum: General 05-08-2010, 03:17 PM
Replies: 13
Views: 9,359
Posted By aguffanti
small and long ncRNAs analysis resources

Hi. You will find extensive informations on small (and large) ncRNA resources in the review in attach.

Kind regards,

Alessandro
Forum: SOLiD 04-30-2010, 07:15 AM
Replies: 6
Views: 3,159
Posted By aguffanti
Hi. Use Bioscope maToGff3 conversion and then use...

Hi. Use Bioscope maToGff3 conversion and then use a parsing script - in attach a script I do use for miRNA analysis

HTH,

Alessandro

--

#!/usr/bin/perl
Forum: SOLiD 01-29-2010, 02:29 AM
Replies: 5
Views: 5,085
Posted By aguffanti
color space to base space

Indeed working in CS does have advantages in various context, from miRNA analysis to, correctly, variation detection. However, the question here was specifically on assembly I understood.

I would...
Forum: Introductions 12-23-2009, 09:41 AM
Replies: 373
Views: 151,453
Posted By aguffanti
Hello from Milano

Hello everybody, I am Alessandro from Genomnia, Milano, Italy. I used to work on 454 data analysis and I am now involved with SOLiD. I hope we will have an useful exchange of ideas ! :)
Forum: General 12-23-2009, 09:39 AM
Replies: 13
Views: 9,359
Posted By aguffanti
Hi! you need, to start it, knownTorefSeq (.txt...

Hi! you need, to start it, knownTorefSeq (.txt and .sql)

uc009vfk.1 NM_201530
uc009vfo.1 NM_001037748
uc009vfp.1 NM_001037748
uc009vgb.1 NM_001037748
uc009vgc.1 ...
Forum: SOLiD 12-21-2009, 03:16 PM
Replies: 11
Views: 4,324
Posted By aguffanti
Hi. No apparently he does more than this, but I...

Hi. No apparently he does more than this, but I am testing it just now with genome resequencing fragment.

It is also evident from the doc examples that it actually corrects sequences even without...
Forum: SOLiD 12-21-2009, 12:52 AM
Replies: 5
Views: 5,085
Posted By aguffanti
Why not doing the opposite, ie convert color...

Why not doing the opposite, ie convert color space in sequence space usign the usual rules and after using a standard assembler? I would also ty the SAET tool which has been just posted on the SOLiD...
Forum: SOLiD 12-21-2009, 12:48 AM
Replies: 11
Views: 4,324
Posted By aguffanti
However, you still need a conversion (in the...

However, you still need a conversion (in the current state of the art) from color space to 'pseudo' nucelotides in order to use an assembler like Velvet. They are not number aware. Since I am workink...
Forum: SOLiD 12-15-2009, 09:28 AM
Replies: 11
Views: 4,324
Posted By aguffanti
Yes there is a wrapper around velvet which uses...

Yes there is a wrapper around velvet which uses something like that, it is available on the SOLiD web site. I am also working at something like this, but sloowly

HTH

Alessandro
Forum: SOLiD 12-15-2009, 09:24 AM
Replies: 4
Views: 3,571
Posted By aguffanti
Schemas for rmapper

Hi - you should build something like that, even by hand, it is simple

111101111011111111111111101111111111
111110111110111111111111111110111111

.. etc ..

It is a mask (0 for mismatch, 1 for...
Showing results 1 to 25 of 29

 


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