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Old 08-22-2012, 07:21 AM   #1
Location: Norway

Join Date: Nov 2011
Posts: 23
Default FASTQC overrepresented Kmers:

Hi there,

Could somebody help in better understanding how kmers and overrepresented sequence can be used to get idea about primer/adapter sequence.

Sequence reads (pair end), which was from Illumina.
I did few preprocessing steps:
1) Remove reads with bad Quality flag, as indicated by ":Y" in header.
2) Used Fastq_qulaity_filter to remove low quality reads
fastq_quality_filter -i R1_QC.fastq -o R1_QC_Filter.fastq -q 20 -p 80 -Q 33 -v
fastq_quality_filter -i R2_QC.fastq -o R2_QC_Filter.fastq -q 20 -p 80 -Q 33 -v

3) Now i want to trim (start/last) bases and remove the adapter sequences.
Which i haven't.

I plot these figures using FASTQC (on quality filtered reads), and i have posted the figures from both pair, and this is how the overrepresented Kmers/sequence look.

How can i get info about adapter/primer from these overrepresented Kmers and sequence.

When i map all these sequence to the genome none of them map to the genome, which are possibly adapter sequences. Can there be more than 2 adapter sequences used in the same experiments ?

IF there are over represented Kmers in the edge (start/end), you can always trim the last 5-6 nt, and you will get rid of those Kmers. How do we treat if there are internal overrepresented Kmers.

Thank you for your help in advance !

Attached Files
File Type: pdf Understanding_Primers.pdf (1.31 MB, 105 views)

Last edited by Chirag; 08-22-2012 at 02:01 PM.
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Old 08-23-2012, 06:04 AM   #2
Location: Norway

Join Date: Nov 2011
Posts: 23

Updated Figure
Attached Files
File Type: pdf Understanding_Primers_V2.pdf (1.33 MB, 98 views)
Chirag is offline   Reply With Quote

fastqc, fastx toolkit

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