The module samtools_index creates a file named ${sample_id}.bam.log. This file is incoporated into the MultiQC report as a column titled "% Mapped":
Notice in the above image that there is also a column titled "% Aligned". This column is generated by Hisat2/Star.
These columns present the exact same information, except that they are called separate things and generated by 2 different tools. This is fine with Hisat2, but with Star, the Column created by Samtool's is incorrect:
STAR does not keep reads in the SAM file which are not aligned, whereas Hisat2 does. This makes it have a confusing column which says 100% allignment.
The module samtools_index creates a file named
${sample_id}.bam.log. This file is incoporated into the MultiQC report as a column titled "% Mapped":Notice in the above image that there is also a column titled "% Aligned". This column is generated by Hisat2/Star.
These columns present the exact same information, except that they are called separate things and generated by 2 different tools. This is fine with Hisat2, but with Star, the Column created by Samtool's is incorrect:
STAR does not keep reads in the SAM file which are not aligned, whereas Hisat2 does. This makes it have a confusing column which says 100% allignment.