/Win7-10_comparison

Upgrading a sequencer from window 7 to window 10 has led to the upgrade of one of the Illumina pipelines. After this, we have noticed that the results obtained are not exactly what we expected. It has been decided to compare several output results between the sequencer with windows 7 and the one that has been updated with windows 10. To do this, this little script takes the convenient information from all the samples in a run and merges them into a single VCF file.

Primary LanguageJupyter Notebook

A quality-comparative analysis of NGS data

Upgrading the computers attached to our sequencers has led to the installation of a new Illumina pipeline. We have been asked to analyze whether the results obtained with the new update are similar to those obtained with the previous update. To perform this analysis, we have used two runs (JTHHC and JVJ65), each with 16 samples. We have used this data with the two versions of Illumina and we have carried out a comparative analysis to see their similarities and differences.

Both analysis are very similar but the JVJ65 one is more complete.

The JVJ65 folder consists of a short Jupyter notebook (JVJ65_Merge_all_needed_samples) that gathers the 16 samples in a single file and selects the values that interest us for later analysis.

A second Jupyter notebook (JVJ65_Analysis.ipynb) where the comparative analysis is carried out.