Different alignment rates for MiXCR analyze and MiXCR align

[Januaryyiyue]

Hi,

I previously used MiXCR4.1.2 align, assemble, etc. separately and get an alignment log like this:

Total sequencing reads: 11689853
Successfully aligned reads: 10588551 (90.58%)
...

When I repeat the analysis with MiXCR analyze, my log file looks like this:

Total sequencing reads: 12150553
Successfully aligned reads: 202393 (1.67%)
...

The alignment rates are significantly different, but the resulting clones are almost the same.

Is there a reason why this is the case? If e.g., a previous alignment rate of 50% would be considered acceptable, what percentage should I expect from the new alignment rate?

Thank you!

[mizraelson]

Hi, can you share the exact commands?

[Januaryyiyue]

Sure.

This is the previous command:

module load mixcr/4.1.2
#SBATCH -J batch1_tcr_post_
java -jar /cluster/mixcr/4.1.2/mixcr.jar align -p rnaseq-cdr3 --verbose -s hsa -OallowPartialAlignments=true -OvParameters.geneFeatureToAlign=VGeneWithP -r /cluster/mixcr4/log/LOG_ALIGN_SAMPLE.txt /cluster/barcode_to_header/SAMPLE_barcode_R1.fastq /cluster/barcode_to_header/SAMPLE_barcode_R2.fastq /cluster/mixcr4/alignments/alignments_SAMPLE.vdjca
java -jar /cluster/mixcr/4.1.2/mixcr.jar assemblePartial /cluster/mixcr4/alignments/alignments_SAMPLE.vdjca /cluster/mixcr4/assemble/rescue1_SAMPLE.vdjca
java -jar /cluster/mixcr/4.1.2/mixcr.jar assemblePartial /cluster/mixcr4/assemble/rescue1_SAMPLE.vdjca /cluster/mixcr4/assemble/rescue2_SAMPLE.vdjca
java -jar /cluster/mixcr/4.1.2/mixcr.jar extend /cluster/mixcr4/assemble/rescue2_SAMPLE.vdjca /cluster/mixcr4/assemble/extended_SAMPLE.vdjca
java -jar /cluster/mixcr/4.1.2/mixcr.jar assemble -r /cluster/mixcr4/log/LOG_ASSEMBLE_SAMPLE.txt /cluster/mixcr4/assemble/extended_SAMPLE.vdjca /cluster/mixcr4/assemble/SAMPLE.clns
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones --chains TRA /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/clones/CLONES_TRA_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones --chains TRB /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/clones/CLONES_TRB_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones --chains TRD /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/clones/CLONES_TRD_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones --chains TRG /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/clones/CLONES_TRG_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones -o -t --chains TRA /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/productiveclones/CLONES_TRA_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones -o -t --chains TRB /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/productiveclones/CLONES_TRB_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones -o -t --chains TRD /cluster/mixcr4/assemble/SAMPLE.clns  /cluster/mixcr4/productiveclones/CLONES_TRD_SAMPLE.tsv
java -jar /cluster/mixcr/4.1.2/mixcr.jar exportClones -o -t --chains TRG /cluster/mixcr4/assemble/SAMPLE.clns /cluster/mixcr4/productiveclones/CLONES_TRG_SAMPLE.tsv

And this is the current command:

module load mixcr/4.6.0
mixcr -Xmx80g analyze local:cap-tcr /cluster/fastqlinks/SAMPLE_R1.fastq.gz /cluster/fastqlinks/SAMPLE_R2.fastq.gz /cluster/mixcr4.6.0_analyze/analyze_output/SAMPLE_mixcr_out