Comments (1)
The file final/database/V.fasta
file is the correct one to look at. It should contain all V genes that were found in the sample. For some reason, the discovery process did not work in this case. I am a bit suprised because the reason for this is often that there werenโt enough reads, but this looks quite ok in your case.
We have released version 0.12 of IgDiscover quite recently. It contains many improvements compared to version 0.11. Can you try that version?
IgDiscover works by first generating a lot of V candidates and then trimming down that list to what it thinks are true germline sequences. Version 0.12 of IgDiscover creates a file iteration-01/annotated_V_germline.tab
, which contains all the candidate V sequences, and it will also tell you (in the column why_filtered
) why a candidate was filtered out. Looking at that file would be very helpful in your case. See the documentation.
Also, it would be important to know what you changed in the igdiscover.yaml
file.
from igdiscover-legacy.
Related Issues (20)
- Parse Flash stats fails HOT 3
- Error: No V genes were discovered in this iteration HOT 11
- Docs may need updating for J discovery HOT 2
- Error in rule read_length_histogram HOT 3
- Snakemake workflow problem with symlinks and temp() HOT 4
- Give sensible error message when running init without DISPLAY
- snakemake error HOT 12
- IgDiscover crashes if no arguments are given HOT 1
- Error running against the test data set HOT 3
- IgBlast error HOT 1
- length of CDR1 region is not divisible by three HOT 3
- Complain if the input reads contain non-nucleotide characters/spaces HOT 10
- error about Microsoft Visual C++ on installation HOT 1
- Solving environment: failed HOT 2
- Cannot install IgDiscover on M1 MacBook Pro HOT 3
- IgDiscover crashes with pandas 2.0.0 HOT 5
- error in_rule_read_length_histogram HOT 11
- trouble installing with conda HOT 2
- New IgDiscover repository
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