Question: Where to find the Trinity assembly statistics?
1
gravatar for BioBing
3.8 years ago by
BioBing130
Denmark
BioBing130 wrote:

Sorry if this is a stupid question (I am pretty new to RNAseq and the Galaxy universe :-) )

I just did a de novo assembly with Trinity (PE reads). The run finished with two files, a log and the fasta containing all the sequences. It was my impression (from reading other posts in here + diverse tutorials online) that there also would be an assembly statistics file? Or am I wrong?

Can anyone tell me how to obtain assembly statistics in Galaxy?

Thank you!

denovo rna-seq trinity • 2.4k views
ADD COMMENTlink modified 3.8 years ago by st.ph.n2.5k • written 3.8 years ago by BioBing130
2
gravatar for st.ph.n
3.8 years ago by
st.ph.n2.5k
Philadelphia, PA
st.ph.n2.5k wrote:

There is a perl script that comes with trinity called 'Trinity_Stats.pl' in the 'util' directory of the base installation. Use as 'perl Trinity_Stats.pl your_assembly.fasta > my_stats.txt'.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by st.ph.n2.5k

So, to understand this right, I have to download Trinity and run the Trinity_Starts on my computer and not through usegalaxy.org?

ADD REPLYlink written 3.8 years ago by BioBing130
1

You can find a copy of Trinity_Stats.pl here. I have never run Trinity in Galaxy, so hopefully someone else can add to the post. I've only ever run on the command-line.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by st.ph.n2.5k

Thank you, I will try to learn how to do it with command line

ADD REPLYlink written 3.8 years ago by BioBing130

I run into this trouble:

Can't locate Fasta_reader.pm in @INC

Any ideas?

ADD REPLYlink written 16 months ago by lw1324ilk0
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