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This article mainly shows you "how the third-generation full-length transcripts of Pacbio compare transcripts with genomes". The content is simple and clear. I hope it can help you solve your doubts. Let me lead you to study and learn this article "how to compare transcripts and genomes in the third-generation full-length transcripts of Pacbio."

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

These are all the contents of the article "how to compare transcripts and genomes in the third generation of Pacbio transcripts". Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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