Forum: Bioinformatics
09-04-2014, 03:57 AM
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Replies: 0
Views: 1,269
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Forum: Bioinformatics
02-06-2014, 12:21 AM
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Replies: 1
Views: 1,548
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).
...
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Forum: Bioinformatics
07-11-2013, 07:17 AM
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Replies: 2
Views: 1,682
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Forum: Bioinformatics
07-10-2013, 09:10 AM
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Replies: 2
Views: 1,682
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...
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Forum: Bioinformatics
05-09-2013, 07:55 AM
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Replies: 1
Views: 2,239
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Forum: Bioinformatics
01-22-2013, 12:57 AM
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Replies: 4
Views: 1,982
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Forum: Bioinformatics
01-21-2013, 08:30 AM
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Replies: 4
Views: 1,982
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...
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Forum: Bioinformatics
01-21-2013, 03:28 AM
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Replies: 4
Views: 1,982
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...
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Forum: Bioinformatics
01-10-2013, 02:56 AM
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Replies: 1
Views: 1,150
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Forum: Bioinformatics
12-11-2012, 06:52 AM
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Replies: 1
Views: 2,114
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...
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Forum: Bioinformatics
12-06-2012, 08:34 AM
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Replies: 0
Views: 1,742
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...
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Forum: Bioinformatics
09-07-2012, 03:15 AM
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Replies: 4
Views: 1,792
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Forum: Bioinformatics
09-07-2012, 03:13 AM
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Replies: 4
Views: 1,792
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
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Forum: Bioinformatics
07-25-2012, 07:51 AM
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Replies: 1
Views: 986
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Forum: Bioinformatics
06-04-2012, 12:49 AM
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Replies: 2
Views: 1,566
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Forum: Bioinformatics
06-01-2012, 06:22 AM
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Replies: 2
Views: 1,566
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...
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Forum: Bioinformatics
05-31-2012, 08:28 AM
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Replies: 4
Views: 2,028
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Forum: Bioinformatics
05-30-2012, 04:04 AM
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Replies: 4
Views: 2,028
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Forum: Bioinformatics
05-28-2012, 03:42 AM
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Replies: 2
Views: 993
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?...
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Forum: Bioinformatics
03-20-2012, 08:33 AM
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Replies: 1
Views: 1,970
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...
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Forum: Bioinformatics
01-17-2012, 03:31 AM
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Replies: 1
Views: 1,688
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Forum: Bioinformatics
12-14-2011, 07:17 AM
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Replies: 2
Views: 2,125
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...
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Forum: Bioinformatics
11-25-2011, 01:16 AM
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Replies: 2
Views: 2,105
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...
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Forum: Bioinformatics
11-25-2011, 01:06 AM
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Replies: 3
Views: 2,218
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Forum: Bioinformatics
11-16-2011, 08:25 AM
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Replies: 3
Views: 2,218
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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