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Error! should be at least 1 contig #189
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Hello @james-e-barrett, Could you check that the reference you're using with |
Hi @ArtRand, The reference used was indeed different (somebody else did the alignment). In my .bam file the chromosomes are labelled "1", "2", etc., but in the reference genome I used from UCSC (hg38.fa) they are labelled "chr1", "chr2", etc. Changing the chromosome names in my .bam file fixed this. Using the same reference genome throughout would presumably avoid the problem also. Thanks for your help. |
Great, feel free to re-open this issue if you have any additional questions or encounter another related problem. |
Hi,
I get the following error running
It runs fine without the --ref and --cpg arguments.
Any help appreciated thanks.
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