Trying to figure out what the last line is of samtools idxstats output:
Here are the last few lines,
GL456368.1 20208 266 0 JH584292.1 14945 8 0 JH584295.1 1976 31 0 * 0 0 33800462
Is this an additional unmapped region? Attempted to get the bam file however was unable, not sure of proper notation for samtools view
samtools view -b /Users/possorted_genome.bam * > asterisk.bam
Basic point is looking for a randomly integrated human transgene in a mouse snRNA-seq assembly.
Also can a transgene integrate potentially within an unplaced contig like the ones above, was able to find mouse version of gene by blasting a db of chromosome 13 from mapped reads - but can't find the human even though I know its there.