It was reported that SAM accumulation in S. cerevisiae was increased by improving methionine and ATP availability by MET6 and SAM2 co-expression combined with sodium citrate feeding (Chen et al. 2016).
Results were reported as SAM rankings, fold changes in average expression levels, and Mann-Whitney U-test p-values.
All read matches fulfilling those criteria were reported in SAM file format.
Under these conditions, only one gene was reported by SAM without additional threshold (data not shown) and no gene at a threshold of 1.5 (Table 1).
In this aligner, MEMs are used as seeds to find gapped alignments and final alignments are reported in SAM format (Li et al., 2009) to facilitate the downstream analysis.
Mapping was done using Novoalign (Novocraft) with the following settings: –r All, -t 60, -l 30, and -s 5. Alignments were reported in SAM format and sorted, indexed, and transformed into count tables (number of mapped reads per transcript per sample) with the use of SAMtools (Li et al. 2009).
Novoalign (Novocraft) was used for mapping with the following settings –r ALL, -t 180, -l 30, and -s 5. Alignments were reported in SAM format and sorted, indexed and transformed into count tables (number of mapped reads per transcript per sample) using SAMtools (Li et al. 2009).
(Data from different conditions, e.g., fluid and pellet as well as different surfaces, were simply aggregated together as distinct features for SAM. Markers reported by SAM in both pellet and supernatant fractions were manually identified and represented only once in the list after they were deemed biologically significant).
The 18.5 million figure was reported by Sams on August 3rd, less than week after the 14 million figure was released.
It has been reported that sams genes belong to small gene families in other plant species [ 49- 53].
