Typically in a sequencing experiment a lot of focus is directed towards ensuring that the quality control of fastq files is good. However, equally important is quality checking the mapping. Currently there are a number of cgat specific and external tools that have been developed to assess this.
The aim of this report is to collate the quality statistics generated from these tools accross your bam files following mapping. The pipeline inputs a bam file and then runs the following tools:
| Tools | Description |
|---|---|
| IdxStats | Samtools idxstats is ran and this calculates the number of mapped and unmapped reads per contig. |
| BamStats | This is a CGAT script (bam2stats) that performs stats on a bam file and outputs alignment statistics |
| PicardStats | This runs to CollectRnaSeqMetrics picard tools |
| StrandSpec | Gives a measure of the proportion of reads that map to each strand. Is used to work out strandness of library if unknown |
| nreads | Calculates the number of reads in the bam file. |
| Paired_QC | This contains metrics that are only required for paired end seqencing. Exon validation is perfomred using the cgat script bam_vs_gtf. Most of the statistics concern splicing |