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Thanks for this wonder tool. I'm trying to do CalcBasicStats from TRUST4 output directly, I couldn't use "Convert" because there's no option "-S" for TRUST4. I'm getting following error, could you kindly advise how to process TRUST4 results to use your amazing tool...
[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 9 6.716418e-02 TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG
out_of_frame IGHV1-301 IGHD1-2601 IGHJ6*04 . assemble1 0 for MiXcr input type: Some mandatory columns are absent in the input file., see _vdjtools_error.log for details
Many thanks,
Rosana
The text was updated successfully, but these errors were encountered:
This issue is solved by using: "grep -v out_of_frame TRUST4_report.tsv > TRUST_report_vdjformat.tsv". VDJtools downstream analysis with the filtered file is working fine now...
Please find below response from liulab-dfci/TRUST4.
TRUST4 uses "out_of_frame" in the amino acid field to represent the kind of non-productive CDR3. It seems VDJtools does not recognize this, and you can use "grep -v out_of_frame" to remove those lines.
Hi Mikessh,
Thanks for this wonder tool. I'm trying to do CalcBasicStats from TRUST4 output directly, I couldn't use "Convert" because there's no option "-S" for TRUST4. I'm getting following error, could you kindly advise how to process TRUST4 results to use your amazing tool...
[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 9 6.716418e-02 TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG
out_of_frame IGHV1-301 IGHD1-2601 IGHJ6*04 . assemble1 0 for MiXcr input type: Some mandatory columns are absent in the input file., see _vdjtools_error.log for details
Many thanks,
Rosana
The text was updated successfully, but these errors were encountered: