Question: How To Judge A Gsm Sample Is Pair-End Or Single-End Sequencing?
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gravatar for quge856
7.5 years ago by
quge85650
quge85650 wrote:

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!

• 1.9k views
ADD COMMENTlink modified 7.4 years ago by Matt Shirley9.3k • written 7.5 years ago by quge85650

What is the GSM number?

ADD REPLYlink written 7.5 years ago by Sean Davis26k

for example, GSM915392

ADD REPLYlink written 7.5 years ago by quge85650
1
gravatar for Matt Shirley
7.4 years ago by
Matt Shirley9.3k
Cambridge, MA
Matt Shirley9.3k wrote:

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.

ADD COMMENTlink written 7.4 years ago by Matt Shirley9.3k

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

ADD REPLYlink written 7.4 years ago by quge85650
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