Export read used in alignment

[racng]

Suppose I ran mixcr align with a tag pattern like this: (CELL:N{8})(UMI:N{8})gcgcg(R1:*)atatatat
Is there a way to export the extracted R1 sequence and qualities?
I tried mixcr exportAlignments -f -targetSequences -targetQualities test.vdjca > test.alignments.tsv.
I wasn't sure if there is any additional processing was done to R1, and whether it is equivalent to "targetSequence" in this context.

[mizraelson]

mixcr align aligns the reads to the reference, therefore in the .vdjca file, you will only see the aligned reads. Depending on the preset you used, the file may contain only reads with a complete CDR3 sequence or may also include reads that do not cover the CDR3 but at least cover a part of a V or a J gene. Beyond that, no additional processing has been done to R1 at this stage.

[racng]

What if I used the --write-all tag during the align step. Would that let me export the parsed (R1:*) from aligned and unaligned reads when running exportAlignments -targetSequences?

[mizraelson]

No, everything that comes out of mixcr align has to be at least partially aligned to TCR or BCR sequence.