Mapping MiXCR clones back to fastq reads
Januaryyiyue opened this issue · comments
Hello,
Is there a way to map the MiXCR clones to their specific reads from the input fastq.gz file? Thanks!
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