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Xiaohui Wu
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280
@xiaohui-wu-4141
Last seen 10.3 years ago
Hi all,
I have two libraries of RNA-seq only with polyA of same tissue (leaf
and leaf), and have mapped them to the genome. Most of these reads are
in 3'UTR but not spread over the whole gene body. And the size of
these two libraries are in great difference, like 25,000 reads versus
1250,000 reads. About 40% and 60% of genes only have 1 read in small
lib and bigger one, respectively. Most of the tags are dominated by
only a few genes. I want to combine these two libs for larger one, but
I think I should normalize the read count before pooling them
together.
If use TPM normalization, read count in smaller library will be
multiplied by 50 times, that means the 1-tag gene will become 50-tag
gene, in the small lib, while maybe that gene is also 1-tag gene in
bigger lib, I feel not comfortable that TPM may make skew the read
distribution. Do you have any idea on normalizing the data instead of
TPM?
Thanks a lot in advance.
Regards,
Xiaohui
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