paired reads adaptor trimming

Question

[prostoesh]

Hi! i have 2 files with paied reads (forward and reversed) and i'm wanting to trimm adapters from these reads.

the problem is in fastqc tool - i'm seeing in its output, that forward reads have problems on both adapter content and overrepresented sequences (which provides me an actual secuence of adapter). Thr adaptor here is GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC

but on the reversed reads, fastqc says that there are adapters (at the end of reads) but no overrepresented sequences, hence i don't have a sequence to trimm.

is there a way to define this reversed adapter?

Answer 1

[Govardhan Anande]

You can get all adapters from here

Answer 2

[Govardhan Anande]

if it is illumina sequencing then I think you might have any of the following adapters:

Adaptor1_5p GATCGGAAGAGCACACGTCTGAACTC Adaptor2_5p AGATCGGAAGAGCGTCGTGTAGGGAA Adaptor3_5p TTCCCTACACGACGCTCTTCCGATCT Adaptor4_5p GAGTTCAGACGTGTGCTCTTCCGATC Adaptor1_3p TTCCCTACACGACGCTCTTCCGATCT Adaptor2_3p GAGTTCAGACGTGTGCTCTTCCGATC Adaptor3_3p GATCGGAAGAGCACACGTCTGAACTC Adaptor4_3p AGATCGGAAGAGCGTCGTGTAGGGAA TruSeq-Universal_Adapter_5p AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT TruSeq-Universal_Adapter_3p TCTAGCCTTCTCGCAGCACATCCCTTTCTCACATCTAGAGCCACCAGCGGCATAGTAA

[prostoesh]

yes, there are like libraries, but it seems unreasonable to test all of them - there must a way to tell what adapter fastqc is showing, or which is paired to the one i've found in forward reads

[Govardhan Anande]

You don't have to test them one by one, just put it like :

python2.7 cutadapt-1.8.1/bin/cutadapt -a GATCGGAAGAGCACACGTCTGAACTC -A GAGTTCAGACGTGTGCTCTTCCGATC -a AGATCGGAAGAGCGTCGTGTAGGGAA -A TTCCCTACACGACGCTCTTCCGATCT -a TTCCCTACACGACGCTCTTCCGATCT -A AGATCGGAAGAGCGTCGTGTAGGGAA -a GAGTTCAGACGTGTGCTCTTCCGATC -A GATCGGAAGAGCACACGTCTGAACTC -b GATCGGAAGAGCACACGTCTGAACTC -B GAGTTCAGACGTGTGCTCTTCCGATC -b AGATCGGAAGAGCGTCGTGTAGGGAA -B TTCCCTACACGACGCTCTTCCGATCT -b TTCCCTACACGACGCTCTTCCGATCT -B AGATCGGAAGAGCGTCGTGTAGGGAA -b GAGTTCAGACGTGTGCTCTTCCGATC -B GATCGGAAGAGCACACGTCTGAACTC -m 30 -o out_R1.fastq -p out_R2.fastq input_R1.fastq input_R2.fastq

[prostoesh]

wow, thanks a lot for a whole command! i'm doing this now

can you also give me link for a source for these sequnces? i wounder what other adapters are there