know the reads are paired ends via the dataset?

[arkilis]

How could I know the reads are paired ends via the dataset?

Sometimes, I saw the database looks like


seq743_A01_F_F01.ab1
seq743_A01_R_F01.ab1
...
...

Are those Roche/454 dataset?

Another: are they paired-end reads?

Thanks

[sBeier]

You cannot say anything for sure, just looking on file names. Files are constantly misnamed.
But, guessing from the filenames:
No, those are not 454 reads. The ab1 file format is short for AppliedBiosystems, so originates from one of their machines.
Yes, those are paired-end. At least you can read the _F_ as forward and _R_ as reverse.

[arkilis]

You cannot say anything for sure, just looking on file names. Files are constantly misnamed.
But, guessing from the filenames:
No, those are not 454 reads. The ab1 file format is short for AppliedBiosystems, so originates from one of their machines.
Yes, those are paired-end. At least you can read the _F_ as forward and _R_ as reverse.

Thanks, now I already know they are from Sanger. But is there any way to tell the sequencer just from the data set? cheers,

[sBeier]

Your best guess is to ask whoever sequenced it. There should be information solving all your questions given to you as an information sheet.
If you got it from a database like NCBI-SRA or such, there is "experiment" information that usually lists the platform used.

[arkilis]

Your best guess is to ask whoever sequenced it. There should be information solving all your questions given to you as an information sheet.
If you got it from a database like NCBI-SRA or such, there is "experiment" information that usually lists the platform used.

Yeah, you are right. Best to get from the manifest.