A problem about using Cogent to collapse redundant transcripts in absence of genome about cdna_cupcake

[Magdoll]

Hi @ClearloveMiao ,
Please use polished hq fasta only.

You will need that both as input to Cogent and later, when you have the output of Cogent, map to the output of Cogent and run collapse.
--Liz

[ClearloveMiao]

Hi, @Magdoll ,
Thanks for your reply!

Another problem, before I am going to do collapsing job using polished hq fasta, should I use LorDEC to correct and CD-HIT-est to remove redundant with polished hq fasta?
Or, another way for asking, should the input fasta file of Cogent be processed by LorDEC and CD-HIT-est first?

Thanks for any suggestion!

[Magdoll]

You don't need to run CD-HIT as it is redundant (and not as effective) as the actual collapse scripts (collapse_isoforms_by_sam.py)

You can run LorDEC against the HQ before you run Cogent and/or collapse.

--Liz