Category: "Sequencing"

Create BigWig files with DeepTools

September 18th, 2017
To display data as bar graphs along the genome e.g. in the UCSC genome browser, you can create BigWig files. The underlying Wig format is described in more detail here. BigWig is the binary version (described here), that allows compressing the data and… more »

BCL files

December 30th, 2016
As part of the Primary Analysis Illumina sequencing machines measure the intensity of the channels used for encoding the different bases and identify the most likely base at a given position of a sequencing read (tag). The Real Time Analysis (RTA)… more »

CRAM format

January 7th, 2015
CRAM files are compressed versions of BAM files containing (aligned) sequencing reads. They represent further file size reduction for this type of data that is generated at ever increasing quantities. more »

Barcode Balancing for Illumina Sequencing

November 4th, 2014
HiSeq & MiSeq The HiSeq and MiSeq use a green laser to sequence G/T and a red laser to sequence A/C. At each cycle at least one of two nucleotides for each color channel must be read to ensure proper registration. more »

NGS reads and their Scores

August 1st, 2014
Generating mapping quality scores For each alignment, BWA calculates a mapping quality score, which is the Phred-scaled probability of the alignment being incorrect. The algorithm is similar to MAQ's except that in BWA we assume the true hit can alwa… more »