akshat998 / castle_bug_test_vbeta Goto Github PK

If the .csv contains any headers they are considered elements - we should specify that these files should not have any headers and should be in the format element_name, sequence without any additional columns.

Tested makeCount.py with 151bp reads with Karmen Aguirre in (Livnat Jerby lab) - the script was unable to call alignments, likely because the read adapters were not cropped.

We could consider adding optional arguments that allow reads to be cropped from the start and end so they can be aligned properly, examples below, or see makeCounts.py from HT-recruit-Analyze.

parser.add_argument('-t', '--trim', dest='trim',
                    help='Select the number of bases to trim off start of read; default is 0',
                    type=int, default=0)

parser.add_argument('-l', '--length', dest='read_length',
                    help='Select the number of bases to align post-trim; default is 17',
                    type=int, default=17)