We have xsq files generated in our lab. And I was planning to convert them to .csfasta and .qual files for further analysis, which can be done using XSQTools. In XSQ tools we have a script called convertFromXsq.sh which does exactly that. It has a filter option -f which says that it removes marked reads. I'm not sure what marked reads are and if I should use this option.
Here is the link to the guide (page 9 has the filter option description) -> XSQ Tutorial
Can anyone tell me what it means? Thanks!