How to merge pacbio transcripts using CD-HIT

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CD-HIT merges pacbio transcript

The full-length transcripts of the third generation of Pacbio are screened by isoseq3. After clustering and correction, high-quality transcripts are obtained, which can be merged to some extent.

Using the cd-hit scheme provided in the cDNA_Cupcaake documentation, run the command as follows:

Cd-hit-est-I-o-c 0.99-T 6-G 0-aL 0.90-AL 100-aS 0.99-AS 30

Parameter description:

Input: a high-quality transcribed sequence file output from isoseq 3 of pacbio

Output: exported merge sequence file

-c: sequence similarity, 99% similarity

-T: number of threads, 6 threads

-G: the comparison strategy adopted. The default is 1, and the global alignment is used. This place is set to 0 and the local alignment strategy will be used.

-aL: coverage of long sequences, set to 90%

-AL: the length of the coverage area of the long sequence, set to the minimum 100bp

-aS: coverage of short sequences, set to 99%

-AS: the minimum length of the coverage area of a short sequence, set to 30bp

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