From trash to treasure: detecting unexpected contamination in unmapped NGS data
Abstract Background Next Generation Sequencing (NGS) experiments produce millions of
short sequences that, mapped to a reference genome, provide biological insights at
genomic, transcriptomic and epigenomic level. Typically the amount of reads that correctly
maps to the reference genome ranges between 70% and 90%, leaving in some cases a
consistent fraction of unmapped sequences. This' misalignment'can be ascribed to low
quality bases or sequence differences between the sample reads and the reference …
short sequences that, mapped to a reference genome, provide biological insights at
genomic, transcriptomic and epigenomic level. Typically the amount of reads that correctly
maps to the reference genome ranges between 70% and 90%, leaving in some cases a
consistent fraction of unmapped sequences. This' misalignment'can be ascribed to low
quality bases or sequence differences between the sample reads and the reference …
[PDF][PDF] From trash to treasure: detecting unexpected contamination in unmapped NGS data
llaria Granata, M Sangiovanni, AS Thind… - PeerJ Preprints, 2017 - peerj.com
Standard procedures for NGS data analysis involve a pre-processing step of reads quality
assessment, followed by the alignment of the filtered reads to a reference genome. Typically
the amount of reads that correctly maps to the specific reference genome ranges between
70% and 90%, leaving in some cases a consistent fraction of unmapped sequences.
Investigating the reasons of this discrepancy may provide relevant information about the
source of the so called unmapped reads. It is not unusual that genetic material of …
assessment, followed by the alignment of the filtered reads to a reference genome. Typically
the amount of reads that correctly maps to the specific reference genome ranges between
70% and 90%, leaving in some cases a consistent fraction of unmapped sequences.
Investigating the reasons of this discrepancy may provide relevant information about the
source of the so called unmapped reads. It is not unusual that genetic material of …