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Filtering reads

In this exercise, you will further clean-up the data by removing reads with low-quality alignments. To be able to do this you need to load alignment qualities from the BAM file. These are stored in the mapq field.

Bu egzersiz

ChIP-seq with Bioconductor in R

kursunun bir parçasıdır
Kursu Görüntüle

Egzersiz talimatları

  • Load reads with information about the alignment qualities attached to each read.
  • Identify all alignments with a quality of at least 20.
  • Create a boxplot comparing alignment quality distributions between the high and low-quality groups.
  • Remove all low-quality alignments.

Uygulamalı interaktif egzersiz

Bu örnek kodu tamamlayarak bu egzersizi bitirin.

# Load reads with mapping qualities by requesting the "mapq" entries
reads <- readGAlignments(bam_file, param=ScanBamParam(what=___))

# Identify good quality alignments
high_mapq <- mcols(reads)$mapq >= ___

# Examine mapping quality distribution for high and low quality alignments
___(mcols(reads)$mapq ~ high_mapq, xlab="good quality alignments", ylab="mapping quality")

# Remove low quality alignments
reads_good <- subset(reads, ___)
Kodu Düzenle ve Çalıştır