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Forum: Bioinformatics 09-04-2014, 03:57 AM
Replies: 0
Views: 1,306
Posted By desmo
Intrasample exon analysis of RNA-Seq data using RPKM values

Hello SeqAns community,

I have been using Mapsplice and RSEM to analyze RNA-Seq data.
The output of my pipeline are the expected counts (or raw count) for genes and isoforms and RPKM values for...
Forum: Bioinformatics 02-06-2014, 12:21 AM
Replies: 1
Views: 1,595
Posted By desmo
How the GQ of a SNP is calculated by UnifiedGenotyper?

Hi, I'm trying to understand how does UnifiedGenotyper usually calculate the GQ of a SNP.
I understood the model to calculate the Likelihood of all the genotypes (AA,AC, AG,AT,CC,CG,CT,GG,GT,TT).
...
Forum: Bioinformatics 07-11-2013, 07:17 AM
Replies: 2
Views: 1,711
Posted By desmo
Really thanks rbagnall. It worked great. ...

Really thanks rbagnall.
It worked great.
Thanks again :)
Forum: Bioinformatics 07-10-2013, 09:10 AM
Replies: 2
Views: 1,711
Posted By desmo
Lightbulb Table of transcript variant 1

Hi all,
I really hope that someone could help me.
I would like to have a table that reports the information about the all the transcripts with the additional information of the number of the...
Forum: Bioinformatics 05-09-2013, 07:55 AM
Replies: 1
Views: 2,270
Posted By desmo
Cool Estimate contamination in Next Generation Sequencing data

Hi everyone,
I'm a bioinformatician and I'm working on cancer genomes.
I would like to know how I can estimate the contamination rate both of the tumor and normal sample of the patient that we will...
Forum: Bioinformatics 01-22-2013, 12:57 AM
Replies: 4
Views: 2,004
Posted By desmo
Cool Thanks. It works great. And thanks for let me...

Thanks. It works great. And thanks for let me know about biopieces, it looks really helpful.
Forum: Bioinformatics 01-21-2013, 08:30 AM
Replies: 4
Views: 2,004
Posted By desmo
Thanks Maasha, your suggestion was really...

Thanks Maasha,
your suggestion was really good. I've installed biopieces and it works great but I have one more question. Do you know how to run biopieces from a perl script? I need it to solve my...
Forum: Bioinformatics 01-21-2013, 03:28 AM
Replies: 4
Views: 2,004
Posted By desmo
Question Extract reads with a specific mutation

Hi everyone,
I would like to extract from a bam file all the reads that are carrying a specific mutation.
I know that samtools give the possibility to extract reads in a specific region, but if I...
Forum: Bioinformatics 01-10-2013, 02:56 AM
Replies: 1
Views: 1,162
Posted By desmo
Smile Available tumor-normal dataset with result (CNV, Snp and Indels)

Hi everyone.
I'm working on cancer genomes analisys and I would like to test the result of my pipeline.
Do you know where I can find some available dataset (something like NCBI sra) that have...
Forum: Bioinformatics 12-11-2012, 06:52 AM
Replies: 1
Views: 2,150
Posted By desmo
VarScan2 somatic output (genotype call)

Hi everyone,
I'm using varscan2 to call somatic variants.
I have some problem to undestand some field of the output, in particular I don't understand what kind of codify they use both for genotype...
Forum: Bioinformatics 12-06-2012, 08:34 AM
Replies: 0
Views: 1,785
Posted By desmo
Cool CNV detector for panel of target gene?

Hi everyone,
I'm working on ngs data produced bu ILLUMINA MySeq (panel of target genes)
I'm searching some tools that perform CNV detection.
I've been looking at CNVnator but it looks that it...
Forum: Bioinformatics 09-07-2012, 03:15 AM
Replies: 4
Views: 1,822
Posted By desmo
There are other database of sequences rather than...

There are other database of sequences rather than NCBI?
Forum: Bioinformatics 09-07-2012, 03:13 AM
Replies: 4
Views: 1,822
Posted By desmo
Available colon cancer cell line?

Does anyone know where I can find an available exome of a colon cancer cell line?
I've tried a search on NCBI (sra) but i didn't find nothing for this specific task.
Thanks in advance to everyone
Forum: Bioinformatics 07-25-2012, 07:51 AM
Replies: 1
Views: 1,000
Posted By desmo
I need some reads to test my pipeline

Hi everyone,
where can I find some raw data (fastq of Illumina) to run my pipeline.
Thanks in advance for your help
Forum: Bioinformatics 06-04-2012, 12:49 AM
Replies: 2
Views: 1,610
Posted By desmo
Thanks for your help. I'll test it as soon as...

Thanks for your help.
I'll test it as soon as possible. Thanks again
Forum: Bioinformatics 06-01-2012, 06:22 AM
Replies: 2
Views: 1,610
Posted By desmo
UCSC Bin indexing system

Does anyone know how exactly works the Bin indexing system used in the UCSC genome browser?
I found just few words in this webpage http://genomewiki.ucsc.edu/index.php/Bin_indexing_system
but i'm...
Forum: Bioinformatics 05-31-2012, 08:28 AM
Replies: 4
Views: 2,059
Posted By desmo
Thanks. I got it!

Thanks. I got it!
Forum: Bioinformatics 05-30-2012, 04:04 AM
Replies: 4
Views: 2,059
Posted By desmo
Download UCSC table with mySql workbench

Does anyone know how to download tables from ucsc server with mysql workbench?
Thanks in advance
Forum: Bioinformatics 05-28-2012, 03:42 AM
Replies: 2
Views: 1,009
Posted By desmo
Post BWA Compression

Hi everybody,
I would like to save each aligned reads in my database using the Bam compression scheme. Does anyone can give me some reference where I can find how exactly bam compression works?...
Forum: Bioinformatics 03-20-2012, 08:33 AM
Replies: 1
Views: 1,982
Posted By desmo
VariantRecalibrator input file error

Hi everyone,
I'm having some trouble with the variant quality score recalibrator.
I have the following error message.

MESSAGE: Bad input: Values for HaplotypeScore annotation not detected for...
Forum: Bioinformatics 01-17-2012, 03:31 AM
Replies: 1
Views: 1,709
Posted By desmo
Problem to install gene pattern on linux from a war file. Help please!!!!

Hi everybody.
I tried several times to install genepattern from the war. file on my pc.
I followed all the step that i found on:
...
Forum: Bioinformatics 12-14-2011, 07:17 AM
Replies: 2
Views: 2,154
Posted By desmo
Post Database of tumor-normal reads

Hi everybody,
I've just started to work on cancer genomic (using ngs) and I would like to test some tools. Unfortunately right now I don't have any available reads.
Anyone knows where I can find...
Forum: Bioinformatics 11-25-2011, 01:16 AM
Replies: 2
Views: 2,195
Posted By desmo
Post Local realignment around indels (454 technology)

Hi everybody, I've worked for one year with Illumina reads but right now I'm working with 454 reads. I used to realign reads around indels with GATK but it doesn't work for Roche technology.
Do...
Forum: Bioinformatics 11-25-2011, 01:06 AM
Replies: 3
Views: 2,258
Posted By desmo
Thanks. I've not yet decided what strategy is...

Thanks. I've not yet decided what strategy is better for my work but yours suggestions were very useful
Forum: Bioinformatics 11-16-2011, 08:25 AM
Replies: 3
Views: 2,258
Posted By desmo
Post Short-read quality control software.

Hi everyone,
I would like to know which are the most useful softwares to control the quality of short reads generated by different kinds of platform.
I've just used FastQC but it's just a visual...
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