I have a mix of both single-end reads and unmerged paired-end reads per sample. I have separated these reads into two different FASTQ files (single and paired end), but have some questions regarding the next stages of my analysis:
1) I am using MALT for alignment. Does MALT need to be 'told' that some files consist of paired end reads?
2) When I import the .rma6 MALT output into MEGAN, how do I inform MEGAN that reads in a file are paired-end? Is there any way to subsequently analyse the alignments from the paired-end and single-end alignments per sample as one sample?