Question: How to get general information of an assembly
0
gravatar for luzglongoria
13 months ago by
luzglongoria40
luzglongoria40 wrote:

Hi there,

I have done my assembly with Trinity and I would like to know whether is there any software for getting general info about the assembly. I would like to know:

Number of bases (total number) Contig length min-max (bp) Median contig length (bp) Mean contig lenghth (bp)

do you know any software that I can use for this purpose?

thank you in advance!

rna-seq assembly software • 322 views
ADD COMMENTlink modified 13 months ago by Buffo1.8k • written 13 months ago by luzglongoria40
2
gravatar for Sej Modha
13 months ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

You could try transrate or rnaQUAST

ADD COMMENTlink written 13 months ago by Sej Modha4.7k

Thank you for the quick response :)

Do they support .fa files?

ADD REPLYlink written 13 months ago by luzglongoria40

They should do, please refer to the manual for more info.

ADD REPLYlink written 13 months ago by Sej Modha4.7k
2
gravatar for Buffo
13 months ago by
Buffo1.8k
Buffo1.8k wrote:

You can also check biopieces:

read_fasta -i assembly.fasta | analyze_assembly -x

ADD COMMENTlink written 13 months ago by Buffo1.8k
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