How to compare transcripts with genomes in the third generation of Pacbio full-length transcripts

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The full-length transcripts of the third generation of Pacbio are analyzed, and the transcripts obtained can be compared with the genome (if there is a genome). There are many software for comparison, so GMAP is recommended.

The method of use is as follows:

Gmap-D / share/nas1/zhangqx/testing/pacbio/ref/gmap-d ipoBat4-f samse-n 0-t 16-- cross-species-- max-intronlength-ends 200000-z sense_force hq.fastq > hq_isoforms.fasta.sam 2 > hq_isoforms.fasta.sam.log

Common parameters are described as follows:

-D: specify the gmap database directory of the reference genome

-d: specify the name in the gmap database

-f: specify the format of the output file

-n: the maximum number of path allowed in the output

-t: number of threads

Cross-species: clippable comparisons with more sensitive algorithms, especially suitable for inter-species comparisons

-- max-intronlength-ends: the maximum distance between the first and last intron

-z: specify the direction of the transcript

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