Question: Script to assess the transcriptome assembly quality in terms of blastx and tblasn results?
0
gravatar for seta
3.9 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Dear all,

As you better know, annotation matrix may be more suitable than length-based matrix for assessing transcriptome assembly quality. I read there is a single script that takes blastx and tblasn results of blasting your assembly against a database of interest and give you all information about the number of unique proteins found in the blastx search, the number of unique contigs hit by proteins in the tblastn search, the number of Reciprocal Best Hits, average Collapse Factor and average Ortholog Hit Ratio. Could anybody please put such a script here? your help would be really appreciated.

sequencing blast rna-seq assembly • 1.8k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by seta1.1k
0
gravatar for rtliu
3.9 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

Trinity:  Full-length transcript analysis for model and non-model organisms using BLAST+

ANGUS 2.0: Scripts, Reciprocal Best-Hits BLAST

CRB-BLAST: Conditional Reciprocal Best Blast

 

 

 

 

ADD COMMENTlink written 3.9 years ago by rtliu2.0k

Thanks friend. I think there should be a script that cover all above-mentioned factor to assess transcriptome assembly quality, has anybody it?

ADD REPLYlink written 3.9 years ago by seta1.1k
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