Question: Is it possible to find a human genome STAR index to not have to create it on my laptop?
0
gravatar for Pin.Bioinf
11 months ago by
Pin.Bioinf170
Malaga
Pin.Bioinf170 wrote:

Hello, I need to map human tumor reads to a reference genome and to do so I need to create the index in STAR. I would have to download the human genome and i dont have enough memory. Does star provide with common genome indexes already generated?

Or is there another solution?

Thank you

ADD COMMENTlink modified 11 months ago by genomax59k • written 11 months ago by Pin.Bioinf170

EDIT: I know its better to generate our own indexes but this is a trial mapping so it's only for teaching purpose and i dont need to be exact

ADD REPLYlink written 11 months ago by Pin.Bioinf170
2

You could limit the needed memory by using only one or two chromosomes. For teaching purpose this should be enough.

ADD REPLYlink written 11 months ago by michael.ante2.8k

Great suggestion. Try the smallest chromosome or failing that even a part of a full chromosome.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax59k

Thank you very much, that is a great solution. But im having a hard time finding the gtf annotation by chromosome: i believe i can get the fasta here: ttp://hgdownload.cse.ucsc.edu/downloads.html#human But no idea on where to find the .gtf to generate the index

Any suggestions?

ADD REPLYlink written 10 months ago by Pin.Bioinf170
1

The gtf contains the chromosome information in the first column. You can download the correct gtf and use grep or awk to extract the lines which correspond to the selected chromosome.

[Update]

You can also use the UCSC table browser to download a certain chromosome from the hg38 scaffold table and the gtf from the GENECODE table. In both cases you can use filters to limit the result to the chromosome of interest and the output format to sequences, resp. gtf.

ADD REPLYlink modified 10 months ago • written 10 months ago by michael.ante2.8k
0
gravatar for genomax
11 months ago by
genomax59k
United States
genomax59k wrote:

@Alex has STAR indexes available at this link.

If your laptop is not able to create indexes then it may not be able to run alignments either. You need ~30G RAM for human samples.

ADD COMMENTlink written 11 months ago by genomax59k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1151 users visited in the last hour