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What is this strand specific pair-end RNA-seq data?

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  • What is this strand specific pair-end RNA-seq data?

    Hi all,

    I downloaded some RNA-seq datasets from NCBI, but some libs have 3 raw files like: (from http://www.ncbi.nlm.nih.gov/sra?term=SRR059171)
    300M SRX022780_SRR059171_1.fastq.bz2
    300M SRX022780_SRR059171_2.fastq.bz2
    11M SRX022780_SRR059171.fastq.bz2
    I know the _1/2 are paired tags, but what is the last file? It is much smaller, some reads in the last file:
    @SRR059171.6873676 SL-XBB:7:120:1786:2047
    NTGGNGTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    +
    !%%%!%%%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    @SRR059171.6873810 SL-XBB:7:120:1790:2045
    NTCCANTNTCTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
    +
    !%%%%!%!%%%%%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    Is that file adaptor sequences? I have no understranding about adaptor, normally when I got the sequences, I just do mapping and further analysis.
    In the nature methods paper used that dataset (Comprehensive comparative analysis of strand-specifc RNA sequencing methods), they mentioned that the adaptors in the NNSR, Hybrid, SMART libs were trimmed and then mapped to the genome.
    But how can I know what and where is the adaptor? Is the adaptor at the 5'-end, like XXXX in read XXXXTTTTTTTTTTTATCG...? And is XXXX in some pattern, like alway AACC?

    Thank you!

  • #2
    I would guess they are unpaired and low quality reads...

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    • #3
      Originally posted by ECO View Post
      I would guess they are unpaired and low quality reads...
      Thank you! At least now I know it is not some conventional RNA-seq file. I'll just use _1 and _2 file for my further analysis.
      About the adaptor, I scanned the start a few nucleotides to see some over-represtented nucleotides to decide the length of the adaptor. Hope this is a correct way to get rid of adaptors.

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