{% extends "template.html" %} {% block table_of_contents %}
Figure 1.1: Ridge plots showing the length distribution of input R1 (left) and R2 (right) reads.
{% endblock %} {% block read_len_table %}Table 1.1: Uniform read lengths for each sample.
Sample | Length R1 | Length R2 |
---|---|---|
{{ row.Sample }} | {{ row.LengthR1 }} | {{ row.LengthR2 }} |
Prior to subsequent analysis, reads are filtered for ambiguous sequence content.
Any read comprised of more than {{"{:.0f}".format(ambiguous_read_threshold * 100)}}% ambiguous bases (N
) is discarded, along with its mate.
(This threshold can be configured with the --ambiguous-thresh
argument.)
The table below shows the number of read pairs that were removed from each sample and which read(s) in the pair exceeded the filtering threshold.
Table 1.2: Metrics for read filtering based on ambiguous content.
Sample | Total Pairs | R1 Only Failed | R2 Only Failed | Pair Failed | Pairs Removed | Pairs Kept | Retention |
---|---|---|---|---|---|---|---|
{{sample}} | {{stats.ambig.total_reads}} | {{stats.ambig.excluded_r1}} | {{stats.ambig.excluded_r2}} | {{stats.ambig.excluded_both}} | {{stats.ambig.excluded}} | {{stats.ambig.retained}} | {{stats.ambig.retention_rate}} |
Paired end reads are merged using FLASh.
Merged reads less than {{"{:,}".format(read_length_threshold)}} bp in length are filtered out prior to read mapping and excluded from all subsequent analysis.
(This threshold can be configured with the --length-thresh
argument.)
Table 2.1: Read merging metrics.
Sample | Filtered Reads | Merged Reads | Merge Rate |
---|---|---|---|
{{sample}} | {{stats.merge.total_reads}} | {{stats.merge.merged_reads}} | {{stats.merge.merge_rate}} |
Figure 2.2: Ridge plot showing the length distribution of merged reads.
Table 2.3: Metrics for read length filtering.
Sample | Total Merged Reads | Reads Removed | Reads Kept | Retention |
---|---|---|---|---|
{{sample}} | {{stats.length.total_reads}} | {{stats.length.excluded}} | {{stats.length.kept}} | {{stats.length.retention_rate}} |
Filtered and merged reads are aligned to marker reference sequences using BWA MEM and formatted, sorted, and indexed using SAMtools.
{% endblock %}