Document files generated

[arisp99]

It would be helpful for users if we could provide a list of all the files that MIPTools generated and a brief description of each one. There are many files generated so it can be confusing navigating them and determining which one will best serve your downstream analysis needs. Although depending on how you use MIPTools, different files may be generated, it would be ideal to have a "master list" of all files.

List of Files

(Generated from two recent runs)

• aligned_haplotypes.csv
• all_barcode_counts.csv
• all_haplotypes.csv
• alternate_AA_table.csv
• alternate_AN_table.csv
• alternate_table.csv
• barcode_counts.csv
• coverage_AA_table.csv
• coverage_AN_table.csv
• coverage_table.csv
• genotypes_AA_table.csv
• genotypes_AN_table.csv
• genotypes_table.csv
• haplotype_counts.csv
• mapped_haplotypes.csv
• offtarget_haplotypes.csv
• reference_AA_table.csv
• reference_AN_table.csv
• reference_table.csv
• repool.csv
• run_meta.csv
• sample_summary.csv
• unique_haplotypes.csv

Please add any files I have missed!

[JeffAndBailey]

Aris, how do you want us to mark this up? Jeff

…

On 11/11/21 21:04, Aris Paschalidis wrote: It would be helpful for users if we could provide a list of all the files that MIPTools generated and a brief description of each one. There are many files generated so it can be confusing navigating them and determining which one will best serve your downstream analysis needs. Although depending on how you use MIPTools, different files may be generated, it would be ideal to have a "master list" of all files. List of Files (Generated from two recent runs) * aligned_haplotypes.csv * all_barcode_counts.csv * all_haplotypes.csv * alternate_AA_table.csv   --> agrregated_AA_alt_cnt.csv * alternate_AN_table.csv  --> agrregated_AA_alt_cnt.csv * alternate_table.csv * barcode_counts.csv * coverage_AA_table.csv   --> aggregate_AminoAcid_coverage_table.csv * coverage_AN_table.csv   --> aggregate_Nucelotide_coverage_table.csv * coverage_table.csv * genotypes_AA_table.csv  --> aggregate_ * genotypes_AN_table.csv * genotypes_table.csv * haplotype_counts.csv * mapped_haplotypes.csv * offtarget_haplotypes.csv * reference_AA_table.csv * reference_AN_table.csv * reference_table.csv * repool.csv  --> repool document * run_meta.csv * sample_summary.csv * unique_haplotypes.csv *Please add any files I have missed!* — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEXH6YK55JNEWDRUAVIHZJLULRY33ANCNFSM5H3YZLJA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[arisp99]

I have created a PR (#19) to address this issue. Please add files generated and their descriptions there. I have already added all the files I mentioned in the original post (without their descriptions).