NGS Formats in GEO database

Question

[xbdr86]

Hi all!

I'm trying to use some data from GEO (GSM652847), but Galaxy is not recognizing it properly. Can you recognize it, it has no heathers.

Thanks!

The data looks like that:

1 1 446 663 GTGAGGACTCGGGAGGTGGAGTCGTACGCCGTCTT 1 1 120 522 TGAGGTAGTAGATTGTACACTTCTTATCGCGTCTT 1 1 122 415 TGAGGTAGTAGGTTGTATAGTATTCGTCTGCCTCT 1 1 112 526 TGAGGTAGTAGATTGTATAGTTTGCGACTGCGTTT 1 1 473 661 GAGAAAGCTCACAAGAACTGCTACCTCCTCGTCTG 1 1 123 364 TGAGGTAGTAGATTGTACAGTTTCTCATCCCCTCT 1 1 243 664 GAAGTTGTTCGTGTTGGATTCAATCGCATACCCTC 1 1 235 389 GTACAGTCCTGTGATAACTGCTCGCATCACGCCTT 1 1 112 222 TCACAGTGAACCGCTCTCATTTCGTATGCGGCCTT 1 1 99 676 TGAGGTAGTAGGTTGTACGGTTTCGTATGCCGTCT 1 1 788 753 GTACAGTACTTGATAACTGATCGCATGCCGTCTTC 1 1 242 224 GGCCTGCCCAGCCCGCACCACTACCCCTCGCCCGG 1 1 113 141 TGAGGTAGTAGGTTGTATGGTTACCTCCTGCCC.C 1 1 460 596 GTACAGTACTGTGATAACTGCTCGTACGCCGCCTT 1 1 606 772 GAGAAAGCTCACAAGAACTGCTACCTCCCCGTTTG 1 1 479 953 GTTCAGGTCACGTCGGGTCGTATGCCGTCTTCTGC

Answer 1

[igor]

That looks like a non-standard format. From the sample description:

supplementary files contain small RNA sequences from purified low molecular weight RNA

[xbdr86]

I don't think that the reason. MiRNA libraries for deep sequencing are purified from gels in order to avoid excessive reads on ribosomal RNA or other extremely abundant molecules. Although the description could sound slightly weirded that's the standard protocol for library generation.

[igor]

I am not saying it's not a standard library prep protocol. I am just saying t's not a standard analysis protocol.