Correcting sample labels and demultiplexing

[ksil91]

1. In the email from Genewiz after the demultiplexing they stated that the barcodes for HC5_11 and NF5_2 in Library 4 (lane 0457) were the same and therefore combined the reads into HC5_11, however on the sample sheet I sent Sam they are different. So we need to search in the undetermined_indices folder for the NF5_2 indexed reads. This also makes me think we should compare the names and indices in the file names to the sample sheet to make sure they are correct.
2. When I was on the last step of the 2brad protocol I accidentally deleted some of the sample names in Library 3 from the "Library" sheet in the master sample sheet. I didn't notice until making the barcode sample sheet and so denoted those on the barcode sheet by putting "w" next to the name. I went back in the sheet revision history to when I plated out the DNA samples and associated the correct name with the well and barcode for these and checked all other samples. Therefore once we double check the names/indices match the barcode sheet we need to change the fastq names for the following samples:
   • HC4_12w -> HC4_11
   • HC4_13w -> HC4_10
   • HC4_15w -> HC4_15
   • HC4_1w -> HC4_7
   • HC4_5w -> HC4_8
   • HC5_1w -> HC5_1
   • SS3_15w -> SS3_20
   • SS3_16w -> SS3_21
   • SS4_1Aw -> SS4_7
   • SS4_1Bw -> SS4_1
   • SS4_3w -> SS4_16
   • SS4_7w -> SS4_9
   • SS4_9 -> SS4_3

I can do these 2 things on the data I've downloaded and put the corrected files in my wetgenes folder.

[sr320]

Has this been resolved?

[ksil91]

I have not done number 1 but have done number 2.

[ksil91]

Check the indices used by Genewiz against our sample sheet, and everything looks ok so I think they must've just inputted the barcode name wrong for NF5_2. Will now search the undetermined indices file for Library 4 to look for NF5_2 samples.