I did a check of my fastq files using fastqc which reavealed several problems: 1) per base gc content, per base sequence content) at the intial part of the 100 bp paired end 2) several over represented sequences and kmer profiles. I then used trimmomatic to remove first 10 base pairs (headcrop 10) which showed some problems in the reads (is it so????) and also supplied Illumina adapters to remove the over represented sequences and kmer profiles using Illuminaclip. The report for overrepresented sequences has been good but the kmer profiles are still existing.
How should I remove those kmer profiles? Is it fine to go ahead and do the alignment to the reference genome without correcting for the kmers?
Thank yop in advance !
I wanted to share the pics/html files, I have got but I am not finding any options to share it on this forum. I am not sure why is that ? Are attachments not allowed on Biostars forum?
- Bishwa K.