Unmapped reads - relative abundance and absolute counts in gene families output

Microbial community profiling HUMAnN
1

Hi,

I ran the following codes

1. to get relative abundance

humann
–metaphlan-options “-t rel_ab --index mpa_vJan21_CHOCOPhlAnSGB_202103
–bowtie2db /home/smeeta.shrestha/metaphlan_data”
–input merged_S1_decon_mm10rm.fq.gz
–output merged_S1_decon_mm10rm_vJan21_RelAb_results

2. to get absolute counts

humann
–metaphlan-options “-t rel_ab_w_read_stats --index mpa_vJan21_CHOCOPhlAnSGB_202103
–bowtie2db /home/smeeta.shrestha/metaphlan_data”
–input / merged_S1_decon_mm10rm.fq.gz
–output merged_S1_decon_mm10rm_vJan21_AbCount_results

However when i look at the genefamilies.tsv output unmapped reads

i get the following :

t rel_ab_w_read_stats|genefamilies|unmapped|3441838|
t rel_ab|genefamilies|unmapped|3436305|

ie there is less unmapped in relative abundance (3436305) compared to absolute abundance (3441838).

~ 5333 difference.

Any insights as what is happening.

Thank you
Smeeta

2

Can you compare the logs for the two HUMAnN runs for other differences? For example, if another species was selected for pangenome mapping from the rel_ab_w_read_stats run relative to the rel_ab run, that could explain why additional reads were mapped.