Hi all,
I am conducting mRNASeq (Illumina HiSeq 2500 with PE data) using Trinity. I am finding it a bit difficult to see if there is an option to provide you with the reads which were not used to create the final .fasta assembly (the 'orphan' reads). Is there a way to do this?
I have considered looking at reads that that did not align back to the assembly, but I'm aware this may not be a true representation of reads not being used in the assembly.
Many thanks
I am conducting mRNASeq (Illumina HiSeq 2500 with PE data) using Trinity. I am finding it a bit difficult to see if there is an option to provide you with the reads which were not used to create the final .fasta assembly (the 'orphan' reads). Is there a way to do this?
I have considered looking at reads that that did not align back to the assembly, but I'm aware this may not be a true representation of reads not being used in the assembly.
Many thanks
Comment