How To Calculate Read Count For Antisense Study?

Question

[M K]

Hi All, I am going to identify antisense for RNAseq using the R package NASTI-seq, but to run this package we should calculate read counts. Does any one know how to do that.

[Dan D]

Do you need to perform the read counts in R? If not, you can easily count the number of reads in a FASTQ file by typing, in bash wc -l [your unzipped FASTQ file] and dividing the result by four. If the file is gzipped, then just type zcat [your gzipped FASTQ file] | wc -l

[M K]

Hi Deedee,

I know how to count read in fastq file. My question is how to calculate them to identifying antisense from mapped data