Question: How to determine number of contigs used in Trinity assembly?
0
gravatar for nikelle.petrillo
2.6 years ago by
Providence College, Providence, RI
nikelle.petrillo90 wrote:

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

assembly rna seq contigs de trinity • 1.8k views
ADD COMMENTlink modified 2.6 years ago by b.nota6.1k • written 2.6 years ago by nikelle.petrillo90
1

Run the following command using your fasta assembly file

  grep -c "^>" trinity_fasta_assembly_file
ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax62k
1
gravatar for st.ph.n
2.6 years ago by
st.ph.n2.4k
Philadelphia, PA
st.ph.n2.4k wrote:

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'

ADD COMMENTlink written 2.6 years ago by st.ph.n2.4k
0
gravatar for b.nota
2.6 years ago by
b.nota6.1k
Netherlands
b.nota6.1k wrote:

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...

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by b.nota6.1k
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