Hello,
I am trying to align metatranscriptome reads to their respective metagenome. It seems that when I run Bowtie2 I run out of memory, but then I use Tophat I am able to complete the alignment. Is Tophat okay to use for environmental samples? What about Cufflinks for differential expression?
I am trying to align metatranscriptome reads to their respective metagenome. It seems that when I run Bowtie2 I run out of memory, but then I use Tophat I am able to complete the alignment. Is Tophat okay to use for environmental samples? What about Cufflinks for differential expression?