Question: Is it possible to find a human genome STAR index to not have to create it on my laptop?
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gravatar for itspilipineiro
3 days ago by
Malaga
itspilipineiro20 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 3 days ago by genomax40k • written 3 days ago by itspilipineiro20

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 3 days ago by itspilipineiro20
2

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

ADD REPLYlink written 3 days ago by michael.ante2.0k

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

ADD REPLYlink modified 3 days ago • written 3 days ago by genomax40k

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 2 days ago by itspilipineiro20

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 2 days ago • written 2 days ago by michael.ante2.0k
0
gravatar for genomax
3 days ago by
genomax40k
United States
genomax40k 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 3 days ago by genomax40k
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