How to align single end multiple lane data using Hisat2?
I have 4 lane , single end reads fastq files per sample that I need to align. How can I combine the 4 lanes to give as input?
I am trying to give the following command:
hisat2 -p 12 -x ./MM10_Index_HISAT/mm10 -U ./Rane_data/Acrolein-1_S4_L1_R1.fastq,./Rane_data/Acrolein-1_S4_L2_R1.fastq,./Rane_data/Acrolein-1_S4_L3_R1.fastq,./Rane_data/Acrolein-1_S4_L4_R1.fastq --rna-strandedness F -S ./HISAT_output
Also, how can I give all samples together in one command? I have 6 samples.
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