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How to determine number of contigs used in Trinity assembly?

Hello,

How do I go about determining how many contigs were used in the de novo trinity assembly i assembled?

Thanks for the help!

Nikelle

trinity de assembly rna-seq
• 5,768 views • link
updated by Ram Ram • written by nikelle.petrillo nikelle.petrillo

Run the following command using your fasta assembly file

  grep -c "^>" trinity_fasta_assembly_file
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written by GenoMax GenoMax

2 answers

There is also a perl script called TrinityStats.pl in the 'util' directory that will give you stats for genes, transcripts, reconstruction size and N metrics. Use as 'perl /path/to/your/install/util/TrinityStats.pl your_assembly.fasta'

• 1 views • link
written by st.ph.n st.ph.n

There is a perl script in the Trinity util folder called "TrinityStats.pl"

You can use it as follow:

perl /trinityrnaseq-2.2.0/util/TrinityStats.pl  /folder2file/Trinity.fasta

Edit: I see @st.ph.n just commented the same solution! Nevermind...

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written by Benn Benn

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