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Where to find the Trinity assembly statistics?

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!

rna-seq trinity denovo
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updated by st.ph.n st.ph.n • written by BioBing BioBing

1 answer

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'.

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written by st.ph.n st.ph.n

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

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written by BioBing BioBing

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.

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written by st.ph.n st.ph.n

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

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written by BioBing BioBing

I run into this trouble:

Can't locate Fasta_reader.pm in @INC

Any ideas?

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written by lw1324ilk • lw1324ilk

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