Run Multiple Fastq files in DNA mode

[thelingxichen]

Hi,

I want to try mixcr on tumor WGS data, but I have multiples fastq files (different run) for one patient.
Like: Run1_fq1.gz Run2_fq1.gz and Run1_fq2.gz Run2_fq2.gz
How can I run mixcr without merging the fastq files?

Thanks,
Lingxi

[dbolotin]

You can try process substitution.

E.g.:

mixcr align -s hs \
    <(gzcat Run1_fq1.gz Run2_fq1.gz) \
    <(gzcat Run1_fq2.gz Run2_fq2.gz) \
    output.vdjca

or zcat in case of linux

Beware that MiXCR can't correctly calculate input size, so progress reporting will be broken, still analysis by itself will not be affected.

[dbolotin]

Please also see docs for WGS analysis pipeline.

[malonzm1]

Hi,

When I run the following:

mixcr analyze 10x-sc-5gex -s hsa --rna --threads 4 --force-overwrite <(zcat SRR7159836/fastq/bamtofastq_R1.fastq.gz SRR7159837/fastq/bamtofastq_R1.fastq.gz) <(zcat SRR7159836/fastq/bamtofastq_R2.fastq.gz SRR7159837/fastq/bamtofastq_R2.fastq.gz) GSM3140593/GSM3140593

I get the following error:

sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `mixcr analyze 10x-sc-5gex -s hsa --rna --threads 4 --force-overwrite <(zcat SRR7159836/fastq/bamtofastq_R1.fastq.gz SRR7159837/fastq/bamtofastq_R1.fastq.gz) <(zcat /SRR7159836/fastq/bamtofastq_R2.fastq.gz SRR7159837/fastq/bamtofastq_R2.fastq.gz) GSM3140593/GSM3140593'

Please advise.

Thanks and good day.

[mizraelson]

I recommend renaming files (or creating links with different names), placing them in the same directory, and using a wildcard:

If you have files like:

SRR7159837_R1.fastq.gz
SRR7159837_R2.fastq.gz
SRR7159836_R1.fastq.gz
SRR7159836_R2.fastq.gz

You can run:

mixcr analyze 10x-sc-5gex \
    -s hsa \
    --rna \
    --threads 4 \
    --force-overwrite \
    SRR{{a}}_{{R}}.fastq.gz \
   GSM3140593/GSM3140593