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I am trying to run Tophat on some Illumina data from an organism
with no UCSC-supported genome. I have taken my Illumina data and run it through the FASTQ groomer. I input this data into tophat, and choose the built-in index option for the reference genome, using an uploaded GenBank FASTA genome. I run this, but when I check the output by running NGS: SAM Tools > flagstat on the bam output from tophat, I get 0% properly paired (see below for the exact output). I have BLASTed the Illumina data just to double-check that I have not mixed files; it is in fact from the organism I am tophat-ing against. I would greatly appreciate input on what I may be doing wrong? Is the "built-in index" supposed to be just the genome sequence in FASTA format or is it something more complex? Thanks Noa 6667700 in total 0 QC failure 0 duplicates 6667700 mapped (100.00%) 0 paired in sequencing 0 read1 0 read2 0 properly paired (-nan%) 0 with itself and mate mapped 0 singletons (-nan%) 0 with mate mapped to a different chr 0 with mate mapped to a different chr (mapQ>=5) |
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