SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
@lisakmalins I tested this out, and overall it looks good!
I did note an issue (on the sample_files_paired_end that's included with the SAMSA2 repo) that the rbind was failing on line 152 of the run_DESeq_stats.R script:
> complete_table <- rbind(complete_table, other_counts_table)
Error in match.names(clabs, names(xi)) :
names do not match previous names
My guess is that this is occurring because the file names aren't being filtered to take off the trailing file extension. The complete_table has names that are just the sample numbers (1, 2, 3, 4), because it splits on underscores and then takes the second element (the one following "control" or "experimental"), in line 51, 55, 62, and 66.
To solve this, I made a couple updates to the way that these script parse the filenames so that it doesn't drop as much of the name as it did in the past, so the complete_table names align with the names in your other_counts_table.
@lisakmalins I tested this out, and overall it looks good!
I did note an issue (on the sample_files_paired_end that's included with the SAMSA2 repo) that the
rbindwas failing on line 152 of therun_DESeq_stats.Rscript:My guess is that this is occurring because the file names aren't being filtered to take off the trailing file extension. The
complete_tablehas names that are just the sample numbers (1, 2, 3, 4), because it splits on underscores and then takes the second element (the one following "control" or "experimental"), in line 51, 55, 62, and 66.To solve this, I made a couple updates to the way that these script parse the filenames so that it doesn't drop as much of the name as it did in the past, so the complete_table names align with the names in your
other_counts_table.