You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Inspection of raw alignments with exportAlignmentsPretty shows that data has the expected architecture, and sample preparation artefacts are not the reason of the problem (if this is the matter of the issue)
It will run all the commands you have, and also assembleContigs that seems to be missing from your pipeline. The output should be as you expected with all regions if covered.
Checklist before submitting the issue:
Expected Result
A clone table with the following fields:
cloneId cloneCount cloneFraction targetSequences targetQualities allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore allVAlignments allDAlignments allJAlignments allCAlignments nSeqFR1 minQualFR1 nSeqCDR1 minQualCDR1 nSeqFR2 minQualFR2 nSeqCDR2 minQualCDR2 nSeqFR3 minQualFR3 nSeqCDR3 minQualCDR3 nSeqFR4 minQualFR4 aaSeqFR1 aaSeqCDR1 aaSeqFR2 aaSeqCDR2 aaSeqFR3 aaSeqCDR3 aaSeqFR4 refPoints
Actual Result
Fewer fields than expected"
cloneId readCount readFraction targetSequences targetQualities allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore allVAlignments allDAlignments allJAlignments allCAlignments nSeqCDR3 minQualCDR3 aaSeqCDR3 refPoints
Exact MiXCR commands
java -jar /path/to/mixcr.jar align -p rnaseq-cdr3 --verbose -s hsa -OallowPartialAlignments=true -OvParameters.geneFeatureToAlign=VGeneWithP -r /path/to/LOG_ALIGN.txt /path/to/file_R1.fastq /path/to/gile_R2.fastq /path/to/alignments_file.vdjca java -jar /path/to/mixcr.jar assemblePartial /path/to/alignments_file.vdjca /path/to/rescue1_file.vdjca java -jar /path/to/mixcr.jar assemblePartial /path/to/rescue1_file.vdjca /path/to/rescue2_file.vdjca java -jar /path/to/mixcr.jar extend /path/to/rescue2_file.vdjca /path/to/extended_file.vdjca java -jar /path/to/mixcr.jar assemble -r /path/to/LOG_ASSEMBLE_file.txt /path/to/extended_file.vdjca /path/to/file.clns java -jar /path/to/mixcr.jar exportClones --chains TRB /path/to/file.clns /path/to/CLONES_TRB_file.tsv java -jar /path/to/mixcr.jar exportClones -o -t --chains TRB /path/to/file.clns /path/to/PROD_CLONES_TRB_file.tsv
The text was updated successfully, but these errors were encountered: