kmer content failling with fastqc
Dear all
I have trimmed my data(illumina 2*150PE) using bbduk from bbmap suite and still have this issue with fastqc (see photos) as failling kmer content, do you have any suggestion to deal with this problem befor downstream analysis?
thank you very much.
• 4,043 views
•
link
written
by
slimane.khayi •
1 answer
• 0 views
•
link
written
by
slimane.khayi •
Log in to answer this question.
More posts like this
-
NOVOPlasty assembly fails with “INVALID SEED” using first read as seed
written by Buddha •
-
FastQC analysis on rrbs
written by Raphael •
-
How to remove illumina universal adapter
written by luckysardar171 •
-
About Fasta rename
written by r00628112 •
-
Multi-records genbank to CDS
written by hazirliver •
-
FastQ check result
written by dpc
-
about Grep the complete sequences containing a specific motif in a fasta file
written by taojincs •
-
goseq pwf length bias plot: help interpreting plot
written by mrodrigues.fernanda •
-
deleted genes (cre-flox) appears in RNAseq analysis
written by supreet0716 •
-
Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
written by sentausa
You did not link a picture, and might read this first.
Please follow these steps to upload pictures How to add images to a Biostars post
did you compare them against the index sequences?
No, how can I proceed ?
In my experience kmer content often seems to fail, and I've never figured out why. Nor has it ever seemed to really matter for downstream assembly etc.
Whilst 5' seems trimmed it looks like 3' is not. Did you trimmed both ends ?
I suggest that you not worry about the
kmercontentfailingand move forward with the analysis. This has been one of the tests that is now turned off by default in newFastQCsince it causes new people to worry for not always valid reasons.Indeed. I have never once seen any sample that has passed all of these FASTQC parameters.
thank you all for your answer.
If you already trimmed both ends you may have to start the trimming over again changing your adapter sequence file. Find your entire repeated sequence in your original reads then do the trimming again with the modified file.