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
5 months ago by
Pin.Bioinf60
Malaga
Pin.Bioinf60 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 5 months ago by genomax49k • written 5 months ago by Pin.Bioinf60

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 5 months ago by Pin.Bioinf60
2

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

ADD REPLYlink written 5 months ago by michael.ante2.5k

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

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax49k

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 5 months ago by Pin.Bioinf60
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 5 months ago • written 5 months ago by michael.ante2.5k
0
gravatar for genomax
5 months ago by
genomax49k
United States
genomax49k 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 5 months ago by genomax49k
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