NCIS scaling script - Githubissues

crazyhottommy / ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

MIT License

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NCIS scaling script #5

Closed gyanmishra closed 7 years ago

gyanmishra commented 8 years ago

I was trying to use NCIS_scaling .R script It doesn’t happen to work on my bam files. problem is happening in this line

ga_ChIP<- readAligned(bamFile, type="BAM") arugment 'type' had value 'BAM' allowable values: 'SolexaExport' 'SolexaAlign' 'SolexaPrealign' 'SolexaRealign' 'SolexaResult' 'MAQMap' 'MAQMapShort' 'MAQMapview' 'Bowtie' 'SOAP'

And still when i give Bowtie argument in type. Its not working

crazyhottommy commented 8 years ago

This script is pretty old and I do not think it is updated. The readGAlignments function in GenomicRanges is preferred. readAligned function is just outdated and maybe not compatible with your bams.