Hello,
I have used Trinity and SOAPdenovo-Trans to assemble my RNA transcriptome data. Using Trinity I can run a subscript (bowtie_PE_separate_then_join.pl) which outputs a bam/bam.bai file that allows me to visiualise the read alignment in each contig using a viewer such as IGV.
Is there a way to produce such a file which I can import into IGV, Tablet or any other viewer using the SOAPdenoco Trans output, i. e. how can I visualise the alignment of reads to the scaffolds?
Thanks
Markus
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