hi all, Is there anyone who can successfully run CERES pipeline in R? [https://github.com/cancerdatasci/ceres][1] [1]: https://github.com/cancerdatasci/ceres

Does anyone have insight into what happens if you apply BQSR twice to a sample? The case here is that we might run a pipeline …

Hi, I work in sunflower (H. annuus) transcriptomics. I'm trying to genotype a big amount of RNAseqs samples from wild accessions (coming from distant places). …

I have performed GATK's Base Quality Score Recalibration (BQSR) on my BAM files. The BQSR has made the per base sequence quality look very bad …

BQSR is recommended at least by [GATK's Best Practices][1] and [Good laboratory practice for clinical next-generation sequencing informatics pipelines][2]. Heng Li [claims][3] that > ...BQSR …

Hello, I have a genomic data file with this format: 1=A, 2=C, 3=G, 0=missing (No "T's") How should I transform this data into SNP (0 …

I'm trying to run BQSR on a sample from a miSeq run, but received an error saying that I need to add read groups. Since …

I am trying to run the genome browser mango that is being developed on top of Adam. https://github.com/bigdatagenomics/mango After installing it as recommended: ``` $ …

The AMPLab at UC Berkeley is looking for senior software developers to work on their BigDataGenomics stack of tools (Apache Spark / SNAP / Adam …

<p>Is there an (semi)official specification and API for Proteomics data? Both for file based and distributed storage?</p> <p>Like there is for Genomics data:</p> <p>Specs:</p> <p>File …