Question: Can I assemble a Eukaryote RNA-Seq using my laptop?
gravatar for utsafar
21 months ago by
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 • 659 views
ADD COMMENTlink modified 21 months ago by russell20 • written 21 months ago by utsafar10

Kallisto will (pseudo) align on a laptop

ADD REPLYlink written 21 months ago by russell20

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

ADD REPLYlink written 21 months ago by genomax43k
gravatar for Antonio R. Franco
21 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

ADD COMMENTlink modified 21 months ago • written 21 months ago by Antonio R. Franco3.5k

I am using this one:

ADD REPLYlink written 16 months ago by utsafar10
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