04 ‐ FAQ

1. Error in fluidigm2PLINK(file = file_path, map = file_path_map, outdir = outdir) : ERROR: You need to fix first the marker names before you can proceed!

There is a marker name mismatch between my fluidigm output and my provided map file This might happen... The function is not designed to fix those mismatches automatically but requires from the user some additional steps to fix those. The most common problem is a mixup of different special characters, e.g. in csv markers are called 'scaffold10:2782', while in the map file they are labelled as 'scaffold10_2782'. The suggested why to fix those is to harmonize the names to one and only character, e.g. '_'. You can do that by running sed in bash e.g. like this

sed -i 's/:/_/g' <filename>

Here, ':' will be substituted with '_'. The -i-option indicates that the file itself will be changed. Hence, take care that you backup your data before running this code to avoid data loss! Never work on the only copy of data you have, especially not if you plan to change the files!