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Editor to share with you how the full-length transcripts of the three generations of Pacbio merge, I believe most people do not know much about it, so share this article for your reference, I hope you can learn a lot after reading this article, let's go to know it!

Pacbio third-generation full-length transcriptome (Iso-Seq) for merging transcripts

In the third-generation transcriptome, when multiple samples are routinely analyzed, transcripts from multiple samples need to be merged into a set of unigene, which can be analyzed using the script "chain_samples.py" in Cupcake.

The script runs with the following command:

Usage: chain_samples.py [- h] [--fuzzy_junction FUZZY_JUNCTION] [--allow_5merge] config_file {norm_fl,norm_nfl,norm_nfl_amb,count_fl,count_nfl,count_nfl_amb}

The input file requires a configuration file.

1. Prepare configuration file

The script needs a configuration file to run. The format of the configuration file is very important, as follows (# is a comment, please ignore it):

# sample name is the name of different samples # path is the directory of different samples for isoforms collapse analysis # prefix is the prefix of the file and needs to be kept consistent in the analysis directory of different samples.

two。 Parameter option

-- fuzzy_junction FUZZY_JUNCTION: this is the maximum number of different bases allowed at the link point.

-- allow_5merge: this is the setting that allows truncation of 5' inconsistent transcripts.

The above is all the contents of the article "how to merge transcripts in the third generation of Pacbio transcripts". Thank you for your 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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