Entering edit mode
6.3 years ago
Pin.Bioinf
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340
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
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
You could limit the needed memory by using only one or two chromosomes. For teaching purpose this should be enough.
Great suggestion. Try the smallest chromosome or failing that even a part of a full chromosome.
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?
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.