Quick question regarding the output files after CASAVA converts them to fastq (from BCL).
We have data from several lanes, and each lane has its own folder (e.g. Project_FC/Sample_lane1 followed by Sample_lane2, etc...).
In each folder, there are several files. The data is paired reads, so we have R1 and R2 for read 1 and read 2 respectively. However, CASAVA splits each read into separate fastq files numbered sequentially, e.g.:
lane1_NoIndex_L001_R1_001.fastq
lane1_NoIndex_L001_R1_002.fastq
lane1_NoIndex_L001_R1_003.fastq
lane1_NoIndex_L001_R1_004.fastq
lane1_NoIndex_L001_R1_005.fastq
lane1_NoIndex_L001_R1_006.fastq
lane1_NoIndex_L001_R1_007.fastq
lane1_NoIndex_L001_R1_008.fastq
lane1_NoIndex_L001_R1_009.fastq
So in this case, going from 001 to 009. In other lanes, it might go from 001 to 011, and so on. Do you know why the fastq files were split up? Is it purely due to the large file size (and if so, can they simply be "cat" together)?
Thanks!
We have data from several lanes, and each lane has its own folder (e.g. Project_FC/Sample_lane1 followed by Sample_lane2, etc...).
In each folder, there are several files. The data is paired reads, so we have R1 and R2 for read 1 and read 2 respectively. However, CASAVA splits each read into separate fastq files numbered sequentially, e.g.:
lane1_NoIndex_L001_R1_001.fastq
lane1_NoIndex_L001_R1_002.fastq
lane1_NoIndex_L001_R1_003.fastq
lane1_NoIndex_L001_R1_004.fastq
lane1_NoIndex_L001_R1_005.fastq
lane1_NoIndex_L001_R1_006.fastq
lane1_NoIndex_L001_R1_007.fastq
lane1_NoIndex_L001_R1_008.fastq
lane1_NoIndex_L001_R1_009.fastq
So in this case, going from 001 to 009. In other lanes, it might go from 001 to 011, and so on. Do you know why the fastq files were split up? Is it purely due to the large file size (and if so, can they simply be "cat" together)?
Thanks!
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