Comments (3)
Before running IgBLAST against the query sequences, IgDiscover runs IgBLAST on the V gene sequences alone in order to find where the FR1/2/3, CDR1/2 regions are located. That is, it delegates finding these regions to IgBLAST.
I believe the .aux
file only contains information about the J genes, so that wouldn’t help here. (Also, IgDiscover forces IgBLAST to use an empty .aux
file anyway.)
IgBLAST will honor the $IGDATA
environment variable, which you can use to point to your own version of the data directory containing the internal_data/
directory with the necessary .ndm.imgt
files. If you need a template, use the directory located at ...your-conda-installation-location/envs/igdiscover/share/igblast/
assuming your IgDiscover environment is named igdiscover
. Be aware IGDATA needs to point to the directory containing the internal_data/
directory, not the internal_data/
directory itself.
The reason the length of the CDR1 regions are not divisible by three is probably that IgDiscover predicted a too short V sequence in a previous iteration, so another, probably easier way to solve the problem is to manually edit the iteration-xx/database/V.fasta
file and add one (or two if needed) made-up nucleotides in the beginning of the problematic sequences.
IgDiscover should really not predict too short V sequences that it then trips over like this in the next iteration, but that is another issue.
from igdiscover-legacy.
Thanks, this is very helpful. In this case the short sequences were mine, not IgDiscover's.
from igdiscover-legacy.
Ah great!
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
- Where is the complete germline DataBase? HOT 1
- 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
- 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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