I'm running Rsubread on a Win10 machine. When running Rsubread (v. 2.0.1) I need to index a cat genome and my output files are wrong. The
.reads file is correct, but the
.files file works for the first 15 chromosomes, then every entry after that is "-1" in column three.
I'm stumped and have searched for days. Is it because I'm using a reference genome with "N" padding? The repeat Threshold for Rsubread defaults to 100, but shouldn't it just skip the Ns and move to genomic sequence? Why does it fail for EVERY chromosome following the first failure?
The results are the same whether I use the cat genome from Ensemble or from NCBI genome, so it isn't the chromosome names. My code is:
> ref <- "cat9.fasta" > buildindex(basename = "cats_index", reference = ref, memory = 10000)
The only messages from Rsubread are:
Check the integrity of provided reference sequences ... || || No format issues were found || || Scan uninformative subreads in reference sequences ... || || **454688 uninformative subreads were found.** || || These subreads were excluded from index building.
The output `cat_index.files` looks like: A1 .//subread-index-sam-010708-934819 67 A2 .//subread-index-sam-010708-934819 246136063 A3 .//subread-index-sam-010708-934819 420465740 B1 .//subread-index-sam-010708-934819 566054919 B2 .//subread-index-sam-010708-934819 777738090 B3 .//subread-index-sam-010708-934819 935629173 B4 .//subread-index-sam-010708-934819 1087876913 C1 .//subread-index-sam-010708-934819 1234814487 C2 .//subread-index-sam-010708-934819 1461317866 D1 .//subread-index-sam-010708-934819 1625197636 D2 .//subread-index-sam-010708-934819 1744806531 D3 .//subread-index-sam-010708-934819 1836496368 D4 .//subread-index-sam-010708-934819 1934995377 E1 .//subread-index-sam-010708-934819 2033125790 E2 .//subread-index-sam-010708-934819 2097678790 E3 .//subread-index-sam-010708-934819 -1 F1 .//subread-index-sam-010708-934819 -1 F2 .//subread-index-sam-010708-934819 -1 MT .//subread-index-sam-010708-934819 -1 X .//subread-index-sam-010708-934819 -1
Thanks for any help!
I edited the title from "index reads" to "index files"