04_compare sequenced data to data from sampling events and make sure as many samples are accounted for as possible

[CecSve]

General check-up when we merge everything (should perhaps be calculated by year):

• [x] how many collected samples from DK?
• [ ] how many collected samples from DE?
• [x] How many of the collected samples were processed in the lab (which were, which weren't)? DK
• [x] How many of the collected samples were processed in the lab (which were, which weren't)? DE
• [x] How many of the processed samples were sequenced DK?
• [ ] How many of the processed samples were sequenced DE?
• [x] How many samples made it through the bioinformatic processing of the sequenced samples DK?
• [ ] How many samples made it through the bioinformatic processing of the sequenced samples DE?

All this should be documented in the supplementary file. In the main manuscript, we should write something in the lines of:

Of the 771 samples collected during June 2018 in Denmark, 561 and in June 2019 678 samples out of 798 collected insect samples were retained for analysis after quality checks in the laboratory and the bioinformatics pipeline (Fig XX (map of sampled areas in DK with transparent dots coloured by year collected), SXX).

Document the output for each country in a comment below.

[CecSve]

• [x] make an output where total samples are merged in the ASV table (change PCRIDs to SampleID_size and combine)

[CecSve]

Question	Answer
how many collected samples from DK?	1358 samples were collected
how many of the collected samples were processed in the lab (which were, which weren't)? DK	2238 size sorted samples were processed in lab (meaning thy got a PCRID). 259 samples were either not sampled or had issues in their metadata so the samples were not processed. 185 samples in the lab data are lab tests, e.g. aliquot test, extraction on ethanol preservative, cleanliness of the nets after wash, and blanks
how many of the processed samples were sequenced DK?	2215 samples were sequenced (including blanks and tests). More samples were sequenced than had biomass etc., noticed duplicates of a few of samples (3 size fraction samples were sequenced twice - could have caused issues in the bioinformatics pipeline!)
How many samples made it through the bioinformatic processing of the sequenced samples DK?	not a question for script 01 but rather for script 01 - but it seems data from library 44 and 36 are missing. 44 we were aware of, not sure what happened to 36 and will investigate

[CecSve]

[PtrsBrt]

Question | Answer -- | -- how many collected samples from DE? | how many of the collected samples were processed in the lab (which were, which weren't)? DE | 234 in 2018 (18 blanks were added and processed) 203 in 2019 (11 blanks) how many of the processed samples were sequenced DE? | How many samples made it through the bioinformatic processing of the sequenced samples DK? |