Closed nielshanson closed 11 years ago
The rRNA stats.txt files in $output/results/rRNA/ seem to report much fewer rRNA sequences than the original .blastout file might suggest. The following output finds 10 hits in the greengenes.blastout file:
shebop:blast_results nielsh$ wc input1.rRNA.greengenes.blastout 10 120 592 input1.rRNA.greengenes.blastout
However, when I look at the input1.greengenes.rRNA.stats.txt file it is reported that only two rRNA sequences were found.
Similarity cutoff : 20.0 Length cutoff : 180 Evalue cutoff : 1e-06 Bit score cutoff : 50.0 Number of rRNA sequences detected: 2 GREENGENES_gg16S-2012-11-06 start end similarity evalue bitscore taxonomy input1_54 94 1347 88.7 0.0 1520.0 k__Bacteria;p__SR1; input1_28 1 1345 81.33 0.0 1042.0 k__Bacteria;p__GN02;c__BB34;
Could you do a sanity check that this is actually correct and that the scripts are not misreporting anything?
-Niels
The BLAST is open-ended without any cutoffs and the .stats.txt file have the BLAST cutoffs applied.
The rRNA stats.txt files in $output/results/rRNA/ seem to report much fewer rRNA sequences than the original .blastout file might suggest. The following output finds 10 hits in the greengenes.blastout file:
However, when I look at the input1.greengenes.rRNA.stats.txt file it is reported that only two rRNA sequences were found.
Could you do a sanity check that this is actually correct and that the scripts are not misreporting anything?
-Niels