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Forum: SOLiD 08-12-2015, 06:46 AM
Replies: 5
Views: 8,149
Posted By wariobrega
Red face Hi Zaag and apologies for the late reply (I...

Hi Zaag and apologies for the late reply (I happened to be on holyday these last couple of weeks!),

Part of the deletions disappeared after I used your options, although new ones reappeared. coll...
Forum: SOLiD 07-01-2015, 01:24 AM
Replies: 5
Views: 8,149
Posted By wariobrega
Hi Linnea, and thanks for the very quick reply! ...

Hi Linnea, and thanks for the very quick reply!

I actually found out a similar answer on the GATK forum after I posted it, but yours was concise and very explanatory, so thank you again!

I'm...
Forum: SOLiD 06-24-2015, 08:28 AM
Replies: 5
Views: 8,149
Posted By wariobrega
GATK Haplotype Caller calls Indels in SOLID reads that IGV does not Display

Hello everyone,

I am Daniele and I'm a Junior Researcher in a private foundation in Rome.

Before explaining my problem, let me say that I am pretty new to the SOLID technology and to Variant...
Forum: Bioinformatics 05-07-2014, 02:49 AM
Replies: 0
Views: 2,517
Posted By wariobrega
Cuffcompare: difference between "nearest_ref" and "oID"

Hello Everyone,

I am a master student new to cufflinks and i am using cuffcompare in order to evaluate an overall analysis on the same samples with and without a GTF Ensembl reference I am...
Forum: General 08-10-2013, 08:10 AM
Replies: 0
Views: 1,767
Posted By wariobrega
Collect Metrics on known and unknown assemblies

Hi everybody,

I have a question to ask about a trivial problem I can't solve.

I am looking for collecting several informations about known assemblies available from ensEMBL

For example, I'd...
Forum: Bioinformatics 09-03-2012, 09:56 AM
Replies: 1
Views: 1,877
Posted By wariobrega
Exclamation Miso Index creator not working with ensEMBL GFF files

Hello everybody.

I am having troubles using the MISO pipeline for finding alternative first exons on my reads dataset.

for making MISO work, an index must be created by the index_gff.py...
Forum: Bioinformatics 09-03-2012, 06:45 AM
Replies: 5
Views: 5,372
Posted By wariobrega
Ty Glados, I found out what was not working!

Ty Glados, I found out what was not working!
Forum: Bioinformatics 08-23-2012, 02:14 AM
Replies: 5
Views: 5,372
Posted By wariobrega
GTF usage in Tophat

I am trying to use Tophat to find novel splicing junction on a zebrafish RNAseq done with the Illumina CAGE-protocol. I am quite novel to the usage of tophat, and I am making several trials to find...
Forum: Bioinformatics 07-03-2012, 01:45 AM
Replies: 12
Views: 28,813
Posted By wariobrega
Thanks a lot for the explanation. So Bowtie 2...

Thanks a lot for the explanation. So Bowtie 2 DOES align the reads in SE that do not align concordantly or discordantly in PE mode. But why this further alignment should be consider useful if it the...
Forum: Introductions 07-02-2012, 06:43 AM
Replies: 0
Views: 935
Posted By wariobrega
A great "Grazie"

Hello to all the SeqAnswers community, my name is Daniele and I'm an MSc student in Bioinformatics in Tor Vergata University in Rome. I am now doing my master thesis project hosted by Prof. Spaink in...
Forum: Bioinformatics 07-02-2012, 06:38 AM
Replies: 12
Views: 28,813
Posted By wariobrega
Bowtie 2 explanation of the pair-end mode report

Hello everybody. I'm a Master Student in Molecular Biology and Bioinformatics and pretty new to NGS technologies. I am using bowtie2 in pair-end mode after using bowtie1 in single end mode on some...
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