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Getting C16 whole embryo files ready for CisGenome
Redownloaded CisGenome and noticed that it was v1.1 so in theory included a ELAND -> ALN conversion executable - except I can not make it work for me. Perhaps the ELAND format is slightly different?
Tried playing around with Access queries for the larger files (chromosomes 1-8, 10 and 11) but gave up.
Converted smaller files manually using Excel and the .bed files that I had to manually rename .txt - erased first two lines, then columns with end point of sequence and everything except direction. Substitute F for + and R for -. Save in tab-delimited format. This worked for first entry with chr18 data, now converting the rest of the files. Cutting up txt files for larger ones manually and pasting into a chr1A and chr1B style file.
Shoot, I tried doing a lot of these, but it's so fast to open and close the command line window, I didn't see what was happening. Apparently the data is not entered. Christelle got to this point last week.