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jodyphelan / NTM-Profiler

Profiling NTM WGS data
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Collate function (summary report multiple samples) #14

Open mdiricks opened 2 years ago

mdiricks commented 2 years ago

Activate collate function to compile list or results for multiple samples. Could e.g. contain samples in rows and "species prediction"; "Warnings"; "resistance prediction macrolides (either S or R)"; "resistance determinant macrolides (e.g. rrl - n.2270A>C ; abs coverage ; rel coverage)" "resistance prediction aminoglycosides"; in seperate columns

jodyphelan commented 2 years ago

You can use ntm-profiler collate to get a combined report, however I think this can potentially improved with more columns liek those you suggested. Do you envisage "Warnings" to show things like low coverage?

id      species closest-sequence        barcode macrolides
ERR115020       Mycobacterium abscessus subsp. massiliense;Mycobacterium abscessus subsp. abscessus     N/A     N/A     N/A
ERR115061       Mycobacterium abscessus subsp. massiliense      N/A     DCC3    rrl_n.2270A>G
SRR6388775      Mycobacterium abscessus subsp. abscessus        N/A     DCC2    erm(41)_resistance_gene
mdiricks commented 2 years ago

You can use ntm-profiler collate to get a combined report, however I think this can potentially improved with more columns liek those you suggested. Do you envisage "Warnings" to show things like low coverage?

id      species closest-sequence        barcode macrolides
ERR115020       Mycobacterium abscessus subsp. massiliense;Mycobacterium abscessus subsp. abscessus     N/A     N/A     N/A
ERR115061       Mycobacterium abscessus subsp. massiliense      N/A     DCC3    rrl_n.2270A>G
SRR6388775      Mycobacterium abscessus subsp. abscessus        N/A     DCC2    erm(41)_resistance_gene

Hi Jody, Looks good. I´ll let you know if I come up with additional columns. Warnings could indeed be low coverage e.g.!