aligning to a very small genome or a single gene

[igor]

I tried to create a separate genome for a single gene (<1 kb). The index is generated fine. However, when I run the alignment, STAR just hangs. It does not exit and there are no errors. The latest progress.out message is "Started 1st pass mapping". Do you know how to resolve this?

I have used STAR in the past to align to small genomes. When the genome gets small enough, the --genomeSAindexNbases parameter needs to be adjusted for genome generation. This does not seem to be the problem.

I then tried adding my separate genome FASTA and GTF file to a common size genome (mm10) as just an extra chromosome. That worked, so my reference files are okay. Why do they do not work on their own then?

I also tried merging them with just a single chromosome of mm10. That also worked, but the alignment took much longer. It seems like as the genome gets smaller or the alignment rate get worse, alignment takes longer. Is there a way to overcome that?

[Alexander Dobin]

Hi Igor,

please send me the Log.out file of the failed run.

Are your reads coming from the big genomes, but you are trying to map to just a small portion of it?

This may indeed by very slow, as STAR is trying hard to "force" the reads into the small sequence (see this post for more discussions https://groups.google.com/d/msg/rna-star/cLpf7BuDnGY/nLXTE_pHDHgJ).

If you are trying to map reads to a single gene sequence, the best strategy would be to add it to the full genome, and then only extract the reads that mapped to it, taking care of the multi-mappers.

Cheers

Alex