Closed Januaryyiyue closed 7 months ago
Hi, yes.
Suppose you are using mixcr analyze
command. Then you should add the following parameters:
mixcr analyze milab-human-rna-ig-umi-multiplex \
-Malign.parameters.saveOriginalReads=true \
-Massemble.clnaOutput=true \
--add-step exportAlignments \
--prepend-export-alignments-field -descrsR1 \
--prepend-export-alignments-field -descrsR2 \
input_R1.fastq.gz \
input_R2.fastq.gz \
results
You will receive a results.alignments.tsv
file with descrsR1
and descrsR2
columns. Instead of a results.clns
file, you'll get a results.clna
file containing information on both alignments and clones.
Furthermore, by using:
mixcr exportAlignments \
-cloneId \
results.clna \
results.alignmentsClones.tsv
You will obtain results.alignmentsClones.tsv
which provides details on both the read header from the original FASTQ file and a cloneId corresponding to the ID in the clonotype table. Records with cloneId -1 were not utilized in the clonotype assembly.
You can also read #1470
Hello,
Is there a way to map the MiXCR clones to their specific reads from the input fastq.gz file? Thanks!