Frequently Asked Questions
Contents:
- Frequently Asked Questions about AbXtract Floes
- What is the difference between upstream and downstream chain designations, _1 and _2?
- What is the difference between upstream and downstream AbXtract floe processing?
- What input formats do the AbXtract upstream processing floes accept, and what are the requirements?
- What is the region of interest (ROI)?
- Where are the liabilities tabulated in AbXtract?
- There are several overlap options available. What are the differences among the different overlap options?
- What input formats do the AbXtract downstream processing floes accept, and what are the requirements?
- How many sequences can the platform process, and what is the output?
- Why is the number of picked representatives below the total number of full-length when using the Automated Top Lead Selection Floe?
- The clustering is taking quite a while with my inputs. Is there a way to bypass clustering in the NGS (PacBio/Illumina) Pipeline Floe?
- I do not need the Floe Report. Can I bypass this option?
- What is a barcode file, barcode_group, barcode_round, and sample_name? How do you format this table?
- What is a customized DNA or AA Database?
- How is relative enrichment calculated?
- How is relative abundance calculated?
- What is meaning of the cluster vocabulary? What is a cluster? What is the difference between cluster and cluster_numeric?
- I have selected the Levenshtein or Hamming Distance Clustering Method. Where do I modify the edit distance?
- How are liabilities quantified, and what do the different liability fields mean?
- What is a customized liabilities table/database, how is it formatted, and does it override the floe parameters?
- How many records are typically handled by the Analyze tool?
- How long does it take to load the Floe Report? Where in Orion can the Floe Reports be found?
- I am having difficulty uploading my FASTQ file or Orion logs out before process is complete, how do I overcome this?
- Why is my download taking so long?
- My floe fails due to a memory allocation issue. How do I overcome this?
- My floe is stalling for more than 48 hours in the NGS (PacBio/Illumina) Pipeline Floe, or beyond the cost level acceptable for this job?
- What happens if I want to change a barcode group after the FASTQ has already been processed or I did not add a barcode group?
- I am having difficulty downloading my file from the dropdown option for my given dataset?
- I processed an AIRR-compatible file and want to link the AbXtract values to the original input values. How can I do that?
- Will annotating my sequences using the NGS (PacBio/Illumina) IgMatcher, Annotation Only - AbXtract Floe give me the same result as my AIRR-compatible file?
- Why are there twice as many records/rows output when I convert a PacBio input to an AIRR-compatible file?