RuiqiaoHe
commented
2 years ago Thanks for you appreciation! The two input files for our pre-processing script are 1) absolute genus abundance matrix, and 2) the number of mapped reads in each sample. The format for the abundance matrix is as follows:
| OTU ID | Sample 1 | Sample 2 | ... | Sample N |
|---|---|---|---|---|
| Taxon 1 | -- | -- | -- | -- |
| Taxon 2 | -- | -- | -- | -- |
| ... | -- | -- | -- | -- |
| Taxon M | -- | -- | -- | -- |
Our pre-processing script de-noised this abundance table for later analyses. The format for the read sum file is as follows:
| id | count |
|---|---|
| Sample 1 | -- |
| Sample 2 | -- |
| ... | -- |
| Sample N | -- |
We used this file to filter samples without enough statistical power. You can use our script and input file as above for your own data. I hope it would be clear for you.
Excellent work and beautiful plots!
My problem: "pre_processing.R" lacks input tables like "L6_abso.txt","fmt_reads_sum" , it will be very nice of you to give any help!