Question: exact command for read normalization using trinity software
1
gravatar for seta
5.7 years ago by
seta1.3k
Sweden
seta1.3k wrote:

Hi all,

I want to do read normalization using trinity, actually with looking the written command in the trinity's site, I'm confused about the allocated RAM to Jellyfish and coverage. It says: 

TRINITY_RNASEQ_ROOT/util/insilico_read_normalization.pl --seqType fq --JM 100G --max_cov 30 --left left.fq --right right.fq \--pairs_together --PARALLEL_STATS --CPU 10.

Could anybody help me to know what means "--JM 100G --max_cov 30". what I understand, 100GB RMA is allocated to Jellyfish that seems is high for computer with 64GB RAM. please let me know the exact command for read normalization in my computer (64GB RAM). Thank a lot in advance

rna-seq assembly • 3.4k views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 5.7 years ago by seta1.3k
2
gravatar for rtliu
5.7 years ago by
rtliu2.1k
New Zealand
rtliu2.1k wrote:

If you want to normalize reads and assemble the transcript with normalized reads (default 50x coverage):

TRINITY_RNASEQ_ROOT/Trinity --normalize_reads --seqType fq --JM 60G --left left.fq --right right.fq --CPU 6

If you want to change the parameter, say --normalize_max_read_cov to 30, add the following to the above command: --normalize_max_read_cov 30

ADD COMMENTlink modified 9 months ago by RamRS28k • written 5.7 years ago by rtliu2.1k

Many thanks to clarify me about it. I think the more read coverage is better, so we don't need to change this parameter, isn't it or is there another story here? 

ADD REPLYlink written 5.7 years ago by seta1.3k

Yes, default 50x is good for many species. See Figure 4 in Trinity Nature Protocols

ADD REPLYlink modified 9 months ago by RamRS28k • written 5.7 years ago by rtliu2.1k

thanks a lot rtliu.

ADD REPLYlink modified 9 months ago by RamRS28k • written 5.7 years ago by seta1.3k
2
gravatar for Brian Bushnell
5.7 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

BBNorm can do normalization with an arbitrarily low amount of memory, and faster than Jellyfish+Trinity.  The exact command to normalize to depth 30 would be:

bbnorm.sh in1=reads1.fq in2=reads2.fq out1=norm1.fq out2=norm2.fq target=30

It will autodetect the amount of memory available and use all of it, but you can add the flag -Xmx50g if you want to restrict it to 50 gigs, for example, or if the autodetection fails due to the system configuration.

ADD COMMENTlink modified 9 months ago by RamRS28k • written 5.7 years ago by Brian Bushnell17k

After normalizing with BBNorm can it then be assembled with Trinity?

ADD REPLYlink written 19 months ago by vsanderl0
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