No alignment using data.extract

[Aliaksandra Radzisheuskaya]

Hello,

I have a sgRNA pattern CACC+G+20 nucleotides+GTT. When I am running this data.extract line, I get 0% aligned reads. Could anyone help solving this?

The sgRNAs in the FASTA files are G+20 nucleotides.

My code is:

data.extract(scriptpath = scriptpath, datapath = datapath,

             fastqfile = fastqfile[1], referencefile = "human_epi", pattern = "CACC(.*(21))GTT", mapping = TRUE, createindex = TRUE)

My output is:

4235022 reads; of these:

  4235022 (100.00%) were unpaired; of these:

    4235022 (100.00%) aligned 0 times

    0 (0.00%) aligned exactly 1 time

    0 (0.00%) aligned >1 times

0.00% overall alignment rate

Thanks,

Alex