#########################################################

FAQ : Flashed and nonflashed reads - what is this ?

#########################################################


  READ COMBINING :

  "Flashed read" : program called "flash" is used to combine the reads (when R1 and R2 overlap) to a single read 
                   "Flashed reads" are the reads the program was able to combine to a single entity (overlap of R1 and R2 reads was found)

  R1
  |------------

      ----------------| R2


  |-------------------| flashed read (combining R1 and R2 to a single entity)


  "Non-flashed read" : program called "flash" is used to combine the reads (when R1 and R2 overlap) to a single read
                   "Non-flashed reads" are the reads the program was not able to combine to a single entity (no overlap of R1 and R2 reads was found)
                   This means : there was no overlap, or the overlap was not "convincing enough" (contained a lot of mismatches, or was very short overlap)

  R1
  |---------

                 -----------| R2


  |---------     -----------| non-flashed read (R1 and R2 cannot be combined, and continue to analysis as separate entities


  These two read sets : "flashed" and "non-flashed" are analysed separately (all result files come "twice" - once for the flashed read set, and once for the non-flashed one)
  Thus, the output files have one Resriction enzyme cut output file for "flashed" reads, and one for "non-flashed" reads. 
  The same goes for bowtie (mapping) results in the .bam files, as well as all subsequent steps.            




Page updated by Jelena 27Sep2017