Where to find the Trinity assembly statistics?
1
1
Entering edit mode
6.0 years ago
BioBing ▴ 150

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 • 4.4k views
ADD COMMENT
2
Entering edit mode
6.0 years ago
st.ph.n ★ 2.7k

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 COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

I run into this trouble:

Can't locate Fasta_reader.pm in @INC

Any ideas?

ADD REPLY

Login before adding your answer.

Traffic: 2168 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6