.bowtie2out.txt file interpretation


I am trying to find the number of alignments my data has done. I am reading the .bowtie2out.txt and I just want clarification over what each column means. I know that each row is an alignment, but within the row, does it contain the number of times that marker had an alignment? If so, which column is that?

Here is a screenshot of part of my output:

Thank you so much!


Hi @jlhaller ,
Thanks for getting in touch. The bowtie2out file contains, for each row, the name of the read (first element) and the marker in the MetaPhlAn database that read mapped against (second element). If you are interested in the alignment, you can keep the SAM file that Bowtie2 will produce using the parameter -s / --samout

Awesome! Thank you so much!