How to remove poly G in Nextseq data
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6.2 years ago
HG ★ 1.1k

I am analyzing a Nextseq run from bacterial data set as like few post earlier here i also found  straight line of G's at the end of the read, can anyone suggest me how to overcome this problem?? any script or tool.

 

 

nextseq assembly trimming • 4.0k views
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6.2 years ago
Asaf 8.6k

I use cutadapt with a poly-G as adapter, you should allow some errors because the poly-G sometimes combine an occasional A-C-T base.

When I analyze paired-end, the second mate is sometimes a poly-G and they I remove it by testing if the read has more than 80% G's. If that's the case I disregard the entire read (or use it as single-end, depends on what I do with it later).

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Thanks for your reply.  For second part of your comment: could you please suggest how i can do such a job any script ?? Because i have 4 paired-end reads for each sample.
 

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What I do is run fastqc and then test if poly-G is one of the over-represented sequences (and for what extent).

Then,actually, cutadapt with poly-G as adapter will remove the read but you should give it both mates as input (I think it will remove both of them but I'm not sure)

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I checked with FastQC as you suggested , in my data set there is no over represent sequence and mean quality score 35. So i hope without any processing the data set i can directly run assembly . What you think?? i used Spades for assembly which also have some error correction steps in ion-hammer. 

   

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Sounds good, I can only dream of getting such numbers. Did you run both files (R1 and R2)?

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Yes i did. I assembled also my data set with a good output N50 value number of contig  

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