Hi all,
I have illumina paired end reads trimmed using Trimmomatic - resulting in 4 files - 2 paired, 2 unpaired (as expected). Now I want to do assembly using SOAPdenovo2. I want to incorporate singleton/unpaired files in addition to paired files for assembly.
There is an option('q') to include singleton files from 'single end files' (which I believe refers to 'single end sequencing' and not paired). But I am not sure if I can use this option for my files where the sequencing is forward-reverse(paired). And if I do use it, should I make reverse complement of my R2_unpaired file before adding it to R1_unapaired and using it further? Or the direction does not matter for singleton files? Do the assembly programs descriminate between complementary strands?
Sorry if the questions are too naive. I am rather new to this.
Thanks in advance.
I have illumina paired end reads trimmed using Trimmomatic - resulting in 4 files - 2 paired, 2 unpaired (as expected). Now I want to do assembly using SOAPdenovo2. I want to incorporate singleton/unpaired files in addition to paired files for assembly.
There is an option('q') to include singleton files from 'single end files' (which I believe refers to 'single end sequencing' and not paired). But I am not sure if I can use this option for my files where the sequencing is forward-reverse(paired). And if I do use it, should I make reverse complement of my R2_unpaired file before adding it to R1_unapaired and using it further? Or the direction does not matter for singleton files? Do the assembly programs descriminate between complementary strands?
Sorry if the questions are too naive. I am rather new to this.
Thanks in advance.
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