RNA seq- exclude genes in y chromosome

Question

[Rob]

Hi friends, I downloaded TCGA-HTseq raw count data for coding genes. is there R-script to exclude genes related to Y chromosome from this data?

Thanks

Answer 1

[Alex Reynolds]

If you are working with BED-formatted data, or a tab-delimited text file with the chromosome in the first column, you could use awk to filter out rows by chromosome name:

$ awk '($1 != "chrY")' in.bed > out.bed

Then read it into R for further processing.

[Rob]

Thanks Alex Reynolds Is this r-code? I could not run this in r. it gives error. This is the error:

Error in .helpForCall(topicExpr, parent.frame()) : 
  no methods for ‘awk’ and no documentation for it as a function