I grabbed the mm9 reference genome from iGenome. When running cuffcompare, I noticed that the genes.gtf refers to chr#_random whereas the chromosome folder only contained chr#, and no files for _random. I corrected this by downloading the chr#_random files from the UCSC mm9 build so now everything matches with the genes.gtf file.
However, the mm9 build came with a pre-index bowtie2 file to use when aligning to the genome (I used TopHat). My concern is that the bowtie2 index was not created with the chr#_random files. Is there a way to check this?
Does anyone know of a better place to grab an accurate mm9 build with bowtie2 index?
If you think the bowtie2 index might be questionable, how can I index all the chromosomes at once to create a version I trust?
Have you guys ran into similar issues?
Thanks a lot for your help.
However, the mm9 build came with a pre-index bowtie2 file to use when aligning to the genome (I used TopHat). My concern is that the bowtie2 index was not created with the chr#_random files. Is there a way to check this?
Does anyone know of a better place to grab an accurate mm9 build with bowtie2 index?
If you think the bowtie2 index might be questionable, how can I index all the chromosomes at once to create a version I trust?
Have you guys ran into similar issues?
Thanks a lot for your help.
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