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do

samtools index ${i}

done

cd ..

5.3.3  Alignment Quality Assessment

After aligning the reads to a reference genome and obtaining the alignment information

in a BAM file, we may need to check the alignment quality before the next step in the data

analysis. The aligned reads may contain duplicate or overrepresented reads produced by

the sequencing process. STAR generates log files that contain some important statistics.

In our example, the log files of each replicate have been saved in “starout” directory. Open

these files and study the statistics included in each file. Figure 5.2 shows alignment statis-

tics in a STAR log file “*final.out”. The log file gives an idea about the mapped reads and

splice sites as well as other important statistics.

FIGURE 5.2  STAR alignment statistics.