Question: Can I assemble a Eukaryote RNA-Seq using my laptop?
0
gravatar for utsafar
19 months ago by
utsafar10
utsafar10 wrote:

I am interested in working on saffron (Crocus sativus). There is a data set related to saffron in SRA database, SRP052616 which contains 5 subsets. I want to assemble its stigma RNA-Seq data, to further work on. SRA file has 4.6G bases and is 3Gb, and when converted to fastq, it is almost 9Gb. Is it possible to assemble this file using my Core i3, 4G RAM, 500G, HDD? If it is possible, please suggest me some applications. I have both windows 7 and Linux Mint 14.7 on my laptop. If it is not possible, please tell me what can I do?

rna-seq saffron assembly • 601 views
ADD COMMENTlink modified 19 months ago by russell20 • written 19 months ago by utsafar10

Kallisto will (pseudo) align on a laptop

https://liorpachter.wordpress.com/2015/05/10/near-optimal-rna-seq-quantification-with-kallisto/ https://pachterlab.github.io/kallisto/

ADD REPLYlink written 19 months ago by russell20
1

While correct this is not a solution to the question being asked in the original post.

ADD REPLYlink written 19 months ago by genomax40k
8
gravatar for Antonio R. Franco
19 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco3.5k wrote:

I don't believe you can do it with such a small computer/s

I see you need to assemble a transcriptome

You can do it using Trinity. The authors of this nice program have set a terrific web service based upon Galaxy that will allow to use Trinity for free for your own assembly. I did it, and it worked very well, and in my case, I used 240Gb of RAM memory. You only need to ask for a login and password. The Galaxy portal is here

https://galaxy.ncgas-trinity.indiana.edu/user/login

ADD COMMENTlink modified 19 months ago • written 19 months ago by Antonio R. Franco3.5k

I am using this one: http://galaxy-qld.genome.edu.au/galaxy

ADD REPLYlink written 14 months ago by utsafar10
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