We recently sequenced a specific mouse strain. The sequencing data was generated on the 5500 XL platform from the same mate-pair library from a single male mouse liver. We had our sequencing done on three flowchips with each using 6,6,3 lanes respectively and generated in total of 15 lanes of data.
I have few doubts regarding the different terminologies used such as sample, group id for my experiment.
My question is related to Readgroup ID (RG), Sample ID (SM) and Library (LB) tags in the SAM format. According to my understanding, the major organizational units for NGS analysis are lane < Library < Sample < Multiple-samples. In other words, multiple libraries (PE,SE or different insert sizes) can be made for the same sample and sequenced using 1 or more lanes. In our case, we have 1 sample (the mouse strain), 1 library (mate pair) and 15 lanes of data. I will align 15 lanes separately and provide a different readgroup ID (RG) tag to each lane as these lanes have beads with same bead ids.
Question: If I want to use mpileup (samtools) or GATK with multiple bam files should I use the same library and sample ID in the header for all the 15 bam files? The machine that has generated 21 lanes has given a different name to samples and library (may be the person who ran the machine did it) even though we used a single mouse and single library. Thats why I am confused.
Thanks a lot for your time.
