Per read info for partial ssAAV and partial scAAV

[dpaudel-tb]

Ask away!

I was looking at the _per_read_info.tsv file and it outputs per read subgenome type. For partials it only lists as Partial. However, the report separates them as Partial_scAAV and Partial_ssAAV. Is there a file where we can get access to which reads are separated as which partials?

[nrhorner]

Hi @dpaudel-tb

The genome subtypes in the *per_read_info.tsv should contain more granular assignments than those you see in the report.

for example, test data results include these this entry:

transgene_cassette_7875	Partial ICG - no ITRs	-	sample_1

Please not note the file is tab-separated, so there are 4 fields here

transgene_cassette_7875
Partial ICG - no ITRs
-
sample_1

Do you see something similar? If not could you send me a snippet of the affected file?

[dpaudel-tb]

Thank you @nrhorner for the details. I was only looking at column 2 and missed the other parts. Looking at the complete breakdown, I am listing below a count of reads for each subtype listed there:

 2940 3` ICG
  97704 3` SBG
    425 3` SBG (incomplete)
     20 3` SBG (incomplete) asymmetrical
     16 3` SBG (incomplete) symmetrical
   3165 3` SBG asymmetrical
   2377 3` SBG symmetrical
 235986 5` ICG
   2863 5` SBG
     31 5` SBG (incomplete)
    139 5` SBG (incomplete) asymmetrical
     60 5` SBG (incomplete) symmetrical
  13908 5` SBG asymmetrical
  15755 5` SBG symmetrical
      1 Assigned_genome_subtype extra_info sample_id
  12805 Complex
  31981 Full_scAAV
  61969 Full_ssAAV
    586 GDM
    566 ITR single strand
    240 ITR1 concatemer ITR1 concatemer
    384 Partial ICG - incomplete ITRs
   8051 Partial ICG - no ITRs
      2 Partial ICG - part of both ITRs
   9043 SBG (unresolved)
     63 Unknown

The qc-report shows the summary as follows:

Assigned_genome_type	count	percentage	sample_id
Partial ssAAV	247947	49.48	unique_nanofilt_q10_l300
Partial scAAV	145506	29.04	unique_nanofilt_q10_l300
Full_ssAAV	61969	12.37	unique_nanofilt_q10_l300
Full_scAAV	31981	6.38	unique_nanofilt_q10_l300
Complex	12805	2.56	unique_nanofilt_q10_l300
ITR region only	806	0.16	unique_nanofilt_q10_l300
Unknown	65	0.01	unique_nanofilt_q10_l300

For the Full_ssAAV, Full_scAAV, and Complex, the count of reads matches the output from per_read_info.tsv. However, for Partial ssAAV and Partial scAAV, I do not see corresponding counts.

[nrhorner]

The partial ssAAV number is aggregated following sub-categories (note: Partial ICG - part of both ITRs is not included, but should be)

2940	 3` ICG
235986	 5` ICG
586	GDM
384	 Partial ICG - incomplete ITRs
8051	 Partial ICG - no ITRs
---
247947    Partial ssAAV

scAAV is aggregated from all the SBG subcategories.

We will be updating the docs soon with some more detailed explanation of the various AAV genome types.

[dpaudel-tb]

Thank you @nrhorner. I was able to map this from the script. Only confusion remained was Partial ICG - part of both ITRs that looks like it is incorrectly reported as Unknown.
Thanks for the clarification.
-Dev

[nrhorner]

No problem. i'll let you know when a fix is out for that incorrect annotation.

Neil