cellranger count前不同Lane的reads能否z
Dear Sir:
Can I zcat all Lanes reads to Lane1 and then run cellranger count？ And Why ？
In 【Specifying Input FASTQ Files for 10x Pipelines】Input FASTQ Files by Lanes 【[Sample Name]S1_L00[Lane Number][Read Type]_001.fastq.gz】.
Can I :
$zcat MySample_S1_L001_R1_001.fastq.gz MySample_S1_L002_R1_001.fastq.gz |gzip > MySample_S1_L001_R1_001.fastq.gz
$ zcat MySample_S1_L001_R2_001.fastq.gz MySample_S1_L002_R2_001.fastq.gz |gzip > MySample_S1_L001_R2_001.fastq.gz
and then run 【cellranger count --fastqs（only S1_L001 ）】? What wrong ? Why not ?
I am looking forward to hearing from you.
Thanks.
Hi Zhou,
Thank you for contacting 10x support.
Theoretically there should be no issue in the concatenation of datasets. However, we have not tested this and it is not a recommended practice. If the correct order of R1 and R2 is not maintained, you may encounter some errors. We have had other users try this in the past, with mixed results. So your analysis may work, but we would urge caution.
Best,
Divya Anjan Kumar
Senior Software Engineer, Field Operations
7068 Koll Center Parkway, Suite 401
Pleasanton, CA 94566 | 10xgenomics.com
(10x Genomics)
Jul 17, 15:06 PDT
