I have been converting a bam file from hg19 to hg38 using CrossMap. This was the code:
python CrossMap.py bam -a hg19ToHg38.over.chain.gz SAMPLE.bam SAMPLE.hg38
Would you please help me interpret this output of CrossMap:
Total alignments:53531694 QC failed: 0 R1 unique, R2 unique (UU) 0 R1 unique, R2 unmapp (UN): 0 R1 unique, R2 multiple (UM): 0 R1 multiple, R2 multiple (MM): 0 R1 multiple, R2 unique (MU): 0 R1 multiple, R2 unmapped (MN): 0 R1 unmap, R2 unmap (NN): 53531694 R1 unmap, R2 unique (NU): 0 R1 unmap, R2 multiple (NM): 0
If all the reads have been unmapped, does this mean that the reads did not align with hg38? Is this a valid bam conversion that I can carry on with to do downstream analysis?