Is it possible to find a human genome STAR index to not have to create it on my laptop?
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
• 7,298 views
•
link
updated
by
Biostar
•
written
by
Pin.Bioinf
•
written
by
Pin.Bioinf
1 answer
@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.
Log in to answer this question.
More posts like this
-
Mapping PCR primers to human genome
written by Yvan •
-
Build Star Index for both Human and Pathogen Reference Genome
written by universe_life •
-
Inserting Junctions Into Genome after Indexing with STAR
written by hkarakurt
-
[STAR] How to clear memory after lost --genomeLoad
written by mathieu.bahin
-
When (not to) pre-build a STAR index
written by jhanks1981 •
-
how many index has to be constructed by STAR for TE analysis
written by lkianmehr
-
how to create .gzi index
written by Omics data mining
-
could not open genomeParameters.txt
written by yueli7
-
indexed human reference genome
written by bioinfo355 •
-
Bwa or bowtie for mapping mulitple genomes
written by williamjohn360
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.