trimmomatic on scRNA seq data

trimmomatic on scRNA seq data

1

Hello
I’m struggling with scRNA pipeline.
I downloaded data from 10* genomics database : support.10xgenomics.com/single-cell-gene expression/datasets/3.0.0/pbmc_1k_v3
when I want to check the size of files I found this :

-rw-r--r-- 1 5062 5000  753851810 Nov  2  2018 pbmc_1k_v3_S1_L001_R1_001.fastq.gz
-rw-r--r-- 1 5062 5000 1772725195 Nov  2  2018 pbmc_1k_v3_S1_L001_R2_001.fastq.gz
-rw-r--r-- 1 5062 5000  748651163 Nov  2  2018 pbmc_1k_v3_S1_L002_R1_001.fastq.gz
-rw-r--r-- 1 5062 5000 1763628623 Nov  2  2018 pbmc_1k_v3_S1_L002_R2_001.fastq.gz

questions:
-it’s normal to find that the size of R1 is not the same as R2 in this case ? in other words pbmc_1k_v3_S1_L001_R1_001.fastq.gz and pbmc_1k_v3_S1_L001_R2_001.fastq.gz should not have the same size ?

-how will the trimmomatic command line will be : is it like this ? or nor because the files have not the same size ? :/

java -jar /opt/conda/envs/scRNA_seq_env/share/trimmomatic-0.39-2/trimmomatic.jar PE input/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L001_R1_001.fastq.gz input/pbmc_1k_v3_fastqs/pbmc_1k_v3_S1_L001_R2_001.fastq.gz output/test/output_forward_paired.fq.gz output/test/output_forward_unpaired.fq.gz output/test/output_reverse_paired.fq.gz output/test/output_reverse_unpaired.fq.gz ILLUMINACLIP:/opt/conda/envs/scRNA_seq_env/share/trimmomatic-0.39-2/adapters/TruSeq3-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 MINLEN:35 SLIDINGWINDOW:4:15

thank you in advance


single


trimmomatic


cell


sequencing


rna

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