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Old 07-05-2017, 05:55 AM   #11
valeu
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Location: Paris

Join Date: Sep 2008
Posts: 69
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Does your new (tab-delimited) .bed file satisfy the requirements listed in the OncoCNV manual?

Check formats:
o reads should be given in .BAM format
o amplicon coordinates should be given in .bed format (with or without the headline) and have amplicon ID in column 4 and gene symbol in column 6, e.g.: chr1 2488068 2488201 AMPL223847 0 TNFRSF14

It is mandatory to provide gene names in the 6th column.

VERY IMPORTANT

Please make sure that:
- There is no duplicates in the coordinates
- Coordinates are sorted
- Gene names are gene names in the sense that corresponding amplicons fall in the same genomic locus and not on different chromosomes
- Gene names cannot be the same as amplicon names or IDs because ONCOCNV assumes to have several amplicons per gene
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