hi,
I confused whether having many independent samples from on animal after and before cancer is the same multiple samples and multiplexed sequencing and multi-library?
Multiplexing is a concept where you mix more than one sample (each appropriately barcoded/tagged). It does not matter where the individual samples come from (from same animal, species, planet).
You could end up making multiple libraries from the same sample (different type, kit, method etc).
Third case would be where you sample a single subject multiple times (before, after, time lapse etc) leading to multiple samples from that entity.
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version 2.3.6
thank you, can we merge bam files from each fastq file (coming from each independent sample from mentioned animal) in exom-sequencing?
If the bam files are from multiple individual fastq file pieces (Illumina by default splits the reads from one sample into 2M read chunks) from a sample, then yes.
Otherwise explain the "independent" sample part more. What is the experiment being done here? If you are looking at changes in that animal over time then you will need to keep them separate.
to identifying any potential mutations arising from an oncogene, we have many independent blood samples with a mouse with induced oncogene before and after leukemia. in exom-seq can I treat each sample as an independent bam file?
How do you propose to do the analysis? Are you only interested in a "before/after" comparison or is there an interest in identifying "when" a mutation(s) first became detectable?
thank you
I think it is about mutations that cause leukemia
actually in project I read; we are interested in development of leukemia. in this mouse with induced oncogene leukemia arises after 10-14 weeks and we suspect that the leukemia is associated with secondary mutations. To identify such mutations, we are performing exome-sequencing. This way, we can compare DNA in blood cells before and after disease. Note, in this setting we can generate many independent leukemias from one ”founder” mouse.
now I got confused whether I should merged bam files after leukemia
Main requirement seems to be "we can compare DNA in blood cells before and after disease" so start with that.
Hi Genomax, What's the possible cost for Multiplexing sequencing for 4096 samples? I am interested to one genomic region (350bp) in 4096 samples? I want to know the cost of this sequencing. Thanks.