How To Judge A Gsm Sample Is Pair-End Or Single-End Sequencing?

Question

[quge856]

Hi there,

When I downloaded GSM sample from GEO, in where can I find the information that whether it's PE sequencing data or not？

Thanks in advance and Merry Christmas!

[Sean Davis]

What is the GSM number?

[quge856]

for example, GSM915392

Answer 1

[Matt Shirley]

This example is an arabidopsis tiling microarray, not short read sequencing data. An example of short read sequence such as GSM320734 actually resolves to the Sequence Read Archive (SRA), and has an associated accession SRX003801 where you may view the "spot descriptor". This diagram will show "forward >>" or "forward >> << reverse" depending on whether the data are paired or single end sequence. GEO datasets that are restricted access may not resolve to the SRA, and for those I am not sure there is an easy way to determine this information.

[quge856]

Thank you man! Your answer dispelled my doubts. So I think the best way is to check the original literature that proposed these data.