Dear community
I have 1080 FASTQ files and I've run them all through FastQC to evaluate their quality.
Then I aggregated the output with the R package fastqcr, which also allowed me to identify distinctingly the sequences found in the module "Overrepresented Sequences". Thus, accross all 1080 files these are the sequences giving troubles:
[1] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATATCTCGTATG TruSeq Adapter, Index 25 "
[2] "ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT Illumina Single End PCR Primer 1 "
[3] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC TruSeq Adapter, Index 4 "
[4] "GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC TruSeq Adapter, Index 4 "
[5] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAAACTCGTATGCC TruSeq Adapter, Index 4 "
[6] "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG Illumina Single End PCR Primer 1 "
[7] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC TruSeq Adapter, Index 7 "
[8] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCAACTCGTATGCC TruSeq Adapter, Index 7 "
[9] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCAGCTCGTATGCC TruSeq Adapter, Index 7 "
[10] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCTCGTATG TruSeq Adapter, Index 21 "
[11] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCGATCTCGTATG TruSeq Adapter, Index 16 "
[12] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCGTATG TruSeq Adapter, Index 15 "
[13] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCC TruSeq Adapter, Index 1 "
[14] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATG TruSeq Adapter, Index 7 "
[15] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC TruSeq Adapter, Index 6 "
[16] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCC TruSeq Adapter, Index 12
To remove the adapters and primers I need to find the correct file to pass on to i.e. Trimmomatic.
Where could I find such file?`
I have gone through several threads and blog posts, but all of them point out the TruSeq Adapters, and I cannot find one with all the corresponding oligos for my sequencing chemistry (I have only been told that the libraries were prepared using TruSeq Nano).
Thanks in advance!