Prepar fastq files at a given barcode.

Source: R/contactsUMI4C.R

Prepar fastq files at a given barcode.

.singlePrepUMI4C(
  fq_R1,
  fq_R2,
  bait_seq,
  bait_pad,
  res_enz,
  prep_dir,
  numb_reads = 1e+09
)

Arguments

fq_R1

Fastq file R1.
fq_R2

Fastq file R2.
bait_seq

Character containing the bait primer sequence.
bait_pad

Character containing the pad sequence (sequence between the bait primer and the restriction enzyme sequence).
res_enz

Character containing the restriction enzyme sequence.
prep_dir

Prep directory.
numb_reads

Number of lines from the FastQ file to load in each loop. If having memory size problems, change it to a smaller number. Default=1e9.

Value

Creates a compressed FASTQ file in wk_dir/prep named basename(Fastq)).fq.gz, containing the filtered reads with the UMI sequence in the header. A data.frame object with the statisitics is also returned.