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Old 09-12-2010, 03:15 PM   #1
xhuister
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Default 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!
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Old 09-12-2010, 05:04 PM   #2
ECO
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I would guess they are unpaired and low quality reads...
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Old 09-14-2010, 06:34 AM   #3
xhuister
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Quote:
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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