Question: Different results for the same data using Trinity. Why?
0
gravatar for tawares07
3.7 years ago by
tawares070
Brazil
tawares070 wrote:

Hi guys!

I used Trinity version (r20140717) twice for the same data (run SRR1462347) and I have got a small difference in the number of assembled transcripts (Trinity.fasta).

How this difference can be explained? Is it acceptable? 

Thank very much!!!

 

 

 

ADD COMMENTlink modified 3.7 years ago by rick.westerman40 • written 3.7 years ago by tawares070

Please post the commands/parameters you used for both runs.

ADD REPLYlink written 3.7 years ago by st.ph.n2.4k

Command:

.../TRINITY/trinityrnaseq_r20140717/Trinity --no_bowtie --seqType fq --JM 40G --left [file_1] --right [file_2] --CPU 10 --output [dir_out]

thanks!

ADD REPLYlink written 3.7 years ago by tawares070

This may be due to using multiple processors. Try using just 1 CPU and I would bet the results are the same. I'm not certain, but this is true for Velvet anyway (i.e., different results with multiple CPUs, same result with 1 CPU).

ADD REPLYlink written 3.7 years ago by SES8.1k

Hi, SES!

I did what you suggested. I will share the results as soon as possible.

Thanks =)

ADD REPLYlink written 3.7 years ago by tawares070
2
gravatar for rick.westerman
3.7 years ago by
United States
rick.westerman40 wrote:

Trinity is non-deterministic.  I believe this arises because of figuring out alternative transcripts will depend on which base transcript you start off with and the starting transcript is random.  Thus small changes are acceptable.  

ADD COMMENTlink written 3.7 years ago by rick.westerman40
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