Analyzing fastq files

  • Created another iPython notebook ‘BSMAP-v1′
  • Used program bsmp-2.74 to compare the files with template genome to observe the methylation pattern.

-a is query file

-d is reference sequence file (In ‘halfshell’ on OWL)

-o is output alignment file (Saved in ‘analyses’ folder in ‘Mrunmayee’ (OWL server))

  • Others used for creating methratio_out_{i}_b.txt files:

-u = report unmapped reads

-z = base quality

-g = gap size

-s = seed size

  • Also used for loop to go through files and count the number of lines to make sure that there is no glitch
  • cd.. = switches directory to one above
  • \ = next line
  • Useful code is in SR github: LabDocs/code/bash.md