From 1d17db7521764e43ec4065846ccd5039c7075fbf Mon Sep 17 00:00:00 2001 From: Meeta Mistry Date: Thu, 2 May 2024 12:11:14 -0400 Subject: [PATCH] Update 05_alignment_QC.md --- lessons/05_alignment_QC.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lessons/05_alignment_QC.md b/lessons/05_alignment_QC.md index 348054a..8844231 100644 --- a/lessons/05_alignment_QC.md +++ b/lessons/05_alignment_QC.md @@ -16,7 +16,9 @@ The next step of QC is where we need to evaluate the quality of the alignments. ## Collecting Alignment Statistics -We are going to use `Picard` once again in order to collect our alignment statistics. `Picard` has many packages for collecting different types of data, but the one we will be using is [`CollectAlignmentSummaryMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360040507751-CollectAlignmentSummaryMetrics-Picard). This tool takes a **SAM/BAM file input** and **produces metrics** (in a tabe delimited `.txt` file) detailing the quality of the read alignments. _Note that these quality filters are specific to Illumina data._ Some exampled of metrics reported include (but, is not limited to): +We are going to use `Picard` once again in order to collect our alignment statistics. `Picard` has many packages for collecting different types of data, but the one we will be using is [`CollectAlignmentSummaryMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360040507751-CollectAlignmentSummaryMetrics-Picard). This tool takes a **SAM/BAM file input** and **produces metrics** (in a tab delimited `.txt` file) detailing the quality of the read alignments. _Note that these quality filters are specific to Illumina data._ + +Some examples of metrics reported include (but, are not limited to): * Total number of reads * Total number of PF (pass-filter) reads (reads that pass an internal qualty fitering on the Illumina sequencer)