normalize between 2 different platform

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8.5 years ago

Edalat ▴ 30

I have some Non-coding RNAseq data with 2 different platform,Illumina Genome Analyzer IIx and Illumina HiSeq 2000,I want to do meta analysis and before that I should normalize them,how should I normalize between 2 different platform?

RNA-Seq • 2.2k views

ADD COMMENT • link updated 12 days ago by linqy ▴ 10 • written 8.5 years ago by Edalat ▴ 30

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I think that the library preparation is more critical than the sequencing machine. If the preparation was different, since each method has its biases, the comparison is not valid.

ADD REPLY • link 8.5 years ago by Asaf 10k

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thank you for a replay.you mean I should investigate their library preparation ?

ADD REPLY • link 8.5 years ago by Edalat ▴ 30

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Yes, exactly. If they're public it's more problematic.

ADD REPLY • link 8.5 years ago by Asaf 10k

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Hello, Could you please tell me whether different datesets generated by multiplex PCR and 5'UMI-tagged 5′-RACE can be analyzed together? The sequence depth is different varying from each other so the abundace analysis seems very comparable. But I am afraid that such difference is caused by differnt sequence methods and platforms. What can I do to normalize these datesets or how can I intergrate these datesets? Could you please give me some suggestions and instructions on how to normalize TCR-seq data? I really need your help!!! Looking forward to your reply. Thanks and best regards, Linqy

ADD REPLY • link 12 days ago by linqy ▴ 10

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