SAMSA: a comprehensive metatranscriptome analysis pipeline

BMC Bioinformatics

Table 2 Read count comparison between single and paired end files

	4012 SR	4012 PE	4015 SR	4015 PE
Forward reads	38,763,820	-	22,613,426	-
Reverse reads	38,763,820	-	22,613,426	-
Paired assembled reads	-	19,269,224	-	7,245,834
Total annotations	11,840,915	21,683,084	1,928,992	3,041,963
Unique annotations	8,658,502	13,310,506	1,280,940	1,875,267

Two pilot paired-end metatranscriptomes were analyzed both in paired configuration, and using only the forward reads (to simulate a single-end metatranscriptome from the same data). Despite higher numbers of total reads, the single-end data matched to fewer total and unique annotations in both cases

ISSN: 1471-2105