Hi,
I'm still getting to know STAR and wanted to ask you, if you just use Chromosomes 1 to 22 and X,Y, MT or also all the other chromosomes with longer names in your fasta reference file for mapping human reads?
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caggtaagtat
Include the various unplaced scaffolds but not the haplotype alleles. The latter will completely screw things up. Including the former will slightly decrease false-positive alignments.
Alright, thank you. So since I'm looking at alternative splicing, including the non-chromosomal fasta file in my genome could may be rewarding than. Do you know where the unplaced scaffolds come from?
The random contigs fall into two groups: those with a known chromosome of origin and those with no known chromosome of origin. In the latter case I presume these actually have multiple copies, though I've never checked. In the former case it's likely that these are regions that just to integrate into the assembly well.
Ok thanks, I will included the fasta files (from ensembl) of chromosome 1-22, X, Y, of mitochondrial and non-chromosomal DNA for my mapping with STAR from now on.
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It depends on what your aim is. If you care about those (I assume you are referring to
random/haplotypetype entries) then you will have to. This may be of interest.Thanks, I'm interested in alternative splicing in human cells.