If you have text files created under DOS/Windows and need to convert the CRLF (carriage return and line feed) characters to LF (line feed) character, here is a quick one-liner.
cat file.txt | perl -ne 's/\x0D\x0A/\x0A/g; print' > file.txt.mod
You can also use dos2unix, however, especially under Cygwin I have seen dos2unix fail without giving any meaningful information about why it was unable to complete the task. In that case, you can just do it by hand.