Big Data with SQLite

Posted Posted in bioinformatics, database, genome informatics

I recently wanted to process genome-wide sequence data that I had extracted into 24 files ranging in size from 3 GB (Gigabytes) for the small chromosome Y to 26 GB for the largest chromosome 1. Further processing this data was challenging as any software script reading the files has to do it in a stream, […]

Read-counting for PGT-A

Posted Posted in bioinformatics, IVF, sequencing

This is an introductory article about Pre-Implantation Genetic Testing for Aneuploidy (PGT-A, formerly known as PGS) using sequencing-based read-counting. The procedure is simplified and I am avoiding to talk about specific companies or products here. Increasing the chances of a successful pregnancy by looking at the embryos chromosomes During an IVF cycle there are in most […]

CRAM format notes

Posted Posted in bioinformatics

CRAM files are compressed versions of BAM files containing (aligned) sequencing reads. They represent a further file size reduction for this type of data that is generated at ever increasing quantities. Where SAM files are human-readable text files optimized for short read storage, BAM files are their binary equivalent, and CRAM files are a restructured […]

BlueFuse Multi Errors

Posted Posted in bioinformatics

When processing microarray or sequencing data with BlueGnome’s / Illumina’s BlueFuse Multi software information and errors are automatically recorded in a log file. By default this should be found in C:\ProgramData\BlueGnome\BlueFuse Multi\blueMarker.log Specifically for the VeriSeq PGS application the following error code might be listed: FailNone = 1, FailInvalidDB = 2, FailInvalidModules = 3, FailPlatform […]