Hello all,
Currently, I am working on a project where we are attempting to determine bacterial biomarkers to see if a predator ate a fresh (predated upon or freshly killed) prey item or a decaying one (i.e., ate carrion). First, we determined a set of ASV's which were associated with only fresh or decaying prey. Now, I would like to match those ASV's to the ones from our predator (stomach and fecal samples) to see how easily we can determine whether that predator consumed fresh or decayed prey.
To do this, I used the excluding sequences by alignment code to obtain a subset table with "hits" that match the ASV's from the prey data set.
(qiime2-2018.8) mcgratse@DESKTOP-0PO1GR1:/mnt/c/Users/Sarah/Desktop/SI-Rat-Project$ qiime quality-control exclude-seqs --i-query-sequences /mnt/c/Users/Sarah/Desktop/SI-Rat-Project/si-rats/rep-seqs-rat-seqs-5.qza --i-reference-sequences /mnt/c/Users/Sarah/Desktop/SI-Rat-Project/chicken_seqs_to_keep.qza --p-method blast --p-perc-identity 0.97 --p-perc-query-aligned 0.97 --o-sequence-hits hits_1.qza --o-sequence-misses misses_1.qza
Saved FeatureData[Sequence] to: hits_1.qza
Saved FeatureData[Sequence] to: misses_1.qza
Then, I filtered my original table to obtain a feature table with only those that hit for use in continued analysis.
(qiime2-2018.8) mcgratse@DESKTOP-0PO1GR1:/mnt/c/Users/Sarah/Desktop/SI-Rat-Project$ qiime feature-table filter-features --i-table /mnt/c/Users/Sarah/Desktop/SI-Rat-Project/si-rats/table-rat-seqs-5.qza --m-metadata-file misses_1.qza --o-filtered-table only-hits-filtered-table.qza
Saved FeatureTable[Frequency] to: only-hits-filtered-table.qza
Here is my original table and my resulting table after filtering.
table-rat-seqs-5.qza (116.4 KB)
only-hits-filtered-table.qza (340.2 KB)
I am still confused as to what this resulting table is really showing me. Is there any data where I can see how the sequences aligned? How do I go from this table to one showing me which ASV's matched where (i.e., ASV42 from prey data set matched to ASV57 in predator data set)? I chose to align at 0.97 and use the blast method based on the online qiime2 documents. Does this make the most sense for what I am trying to do?
Any assistance and/or advice is greatly appreciated!
Thanks,
Sarah