Closed l0ka closed 3 years ago
Hi,
If your bed natively misses "chr" but corresponds to the hg19 genome build, it's probably that it refers to the 1000genomes HS37D5 build (that is available as a BSgenome under bioconductor, package name 'BSgenome.Hsapiens.1000genomes.hs37d5'). That's the genome build used by the Legacy TCGA project, by example. You may have more luck using this genome build ? Could you please give me some feedback then ? I currently wonder what causes the second error :S
Hi @aoumess, luckily it was just a problem of genome version. Using the original bed file (without "chr" notation and the mt chromosome coordinates) and the "BSgenome.Hsapiens.1000genomes.hs37d5" solved both issues. Thank you very much!
P.S.: for some samples, using facets I get this error: https://github.com/mskcc/facets/issues/46 Almost nobody seems to care about it but maybe it could be nice to adjust EaCoN code to prevent this annoying issue.
Hi, thank you for this great (and very easy to use) package. I successfully run EaCoN on SNP array data and now I am trying to analyze WES data. I am currently experiencing some problems at the very first step of the analysis. The command I used is:
BINpack.Maker(bed.file = "S06588914_Regions_coord_only.bed", bin.size = 50, genome.pkg = "BSgenome.Hsapiens.UCSC.hg19")
I tried using both a bed file with and without the "chr" notation on chromosomes, however I always get the following:Without "chr":
With "chr":
The BED file looks like this:
And the chromosomes are:
Session info:
What should I do? Thank you in advance!
[UPDATE]: the chromosome error apparently is due to missing "chr" notation and "chrM" coordinates. The other error is still present.