是人是鼠，你心里没有数？GPL21827之谜

生信技能树

发布于 2019-12-11 10:36:26

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发布于 2019-12-11 10:36:26

文章被收录于专栏：生信技能树

最近在对GEO数据库的全部GPL平台的芯片探针序列进行批量重新注释的时候，发现如果工具芯片自带的物种信息来自动化选择参考基因组，居然还会出现某个芯片探针比对率非常低的情况，比如GPL21827这个平台：

60898 reads; of these:
  60898 (100.00%) were unpaired; of these:
    59099 (97.05%) aligned 0 times
    1753 (2.88%) aligned exactly 1 time
    46 (0.08%) aligned >1 times
2.95% overall alignment rate

因为在GEO数据库，它居然被记录为mouse这个物种，但是它明明是human啊！

Agilent-079487 Arraystar Human LncRNA microarray V4 (Probe Name version)
GPL21827
Public on May 07 2016
2016/5/6
2016/5/7
in situ oligonucleotide
Mus musculus
Agilent Technologies

实在是太诡异了：https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21827

可是我在GEO官网查询它：Agilent-079487 Arraystar Human LncRNA microarray V4 (Probe Name version)

物种又是human。

image-20191203111321663

这并不是唯一的比对率低的情况：

一款circRNA芯片：https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL23467

170351 reads; of these:
  170351 (100.00%) were unpaired; of these:
    169391 (99.44%) aligned 0 times
    811 (0.48%) aligned exactly 1 time
    149 (0.09%) aligned >1 times
0.56% overall alignment rate

一款miRNA芯片 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8180

380 reads; of these:
  380 (100.00%) were unpaired; of these:
    215 (56.58%) aligned 0 times
    138 (36.32%) aligned exactly 1 time
    27 (7.11%) aligned >1 times
43.42% overall alignment rate

当然了，circRNA芯片和miRNA芯片没有注释的必要性了，但是lncRNA和普通的mRNA芯片我都已经搞定啦

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原始发表：2019-12-05，如有侵权请联系 cloudcommunity@tencent.com 删除

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