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Results page currently does not have metadata explaining where data came from.

Having the ability to export the collapsed sequences (based on 99% homology) from each dataset has been helpful. However, I realize now that we still need the output of aligned nucleotide sequences the way old Datamonkey UDS pipeline presented it. To screen for DI, we would like to take random representative samples from each dataset for downstream phylogenetic analysis, and we cannot do that with the collapsed sequence set. Thanks much. Gabe

We would like to submit a specific dataset including NGS sequences from a cohort of MSM pairs (source and recipient).
Is it possible to add a new level (5th) for the pair identification (source / recipient) or to replace the actual optional Level 4 ("replicate", not necessary for our cohort)
Level 1: Patient ID (anything, unique, required)
Level 2: Sample date (YYYYMMDD format, required)
Level 3: Compartment (anything, optional)
Level 4: Replicate (anything, optional)
+/-Level 5: Pair ID (for example: S3 for the Source of Pair #3 or R12 for the recipient of Pair #12...)

thx
Antoine

Hi
Here are several comments about the octamonkey pipeline:
-There are some duplicates with the ID of the sequences in the clusters alignment ('region' column) and there are also some 'space' characters that are conflicting.
-Problems with the colors of the FST figures and no option to download these figures.
-A very brief 'help' page with explanation of each option/output may help (for example, what does the 'divergence column' refer to?)
-Need to add an export option to download all the haplotypes (and not only the consensus) from a cohort.

Many thx for this fantastic job.
A

When attempting to 'Export Consensus Sequences' from ProtC data (>1000 records), it only captured 133 sequences. Looking at individual datasets that were not captured in the export revealed no significant problems; I was able to generate a consensus sequence myself from them.
Thanks!
Gabe

1. Raw read metrics (number of raw reads, how many reads fulfill quality metrics or how many low quality reads are filtered out from subsequent analyses).
2. Number of clean reads per coding region.
   Thanks!
   Gabe

For the Protocol C dataset, it is nice to be able to export individual sequences (major homology clusters). But to be able to export them all 'en masse' would be nice too. There is an 'Export' feature at the top right of the page which allows one to export all sequences (I think), but given the large number of sequences, the uploading portion never finishes.
Thanks,
G

The sequence titles in the downloadable identical sequence alignment should be more informative. Perhaps (in addition to cluster # and # reads collapsed) also include PID, date/Visit code and region.
Request from Antoine/Gabe.
Thanks