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Alignment files are stored in the **ALIGNMENT** folder. They are also indexed with `samtools index` if further analysis on the bam files is needed (e.g. IGV visualization).
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## Expression matrix
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## <a name="expressionMatrix"></a> Expression matrix
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Finally, the bam files are parsed in python script `count.py` with the help of the **pysam** module. The aim is to count each molecule of mRNA captured, with the help of the UMI's, for every gene in every sample, and thus, create an expression matrix.
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