Question: cutadapt: forward and reverse adapter sequence options
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gravatar for umn_bist
3.3 years ago by
umn_bist320
umn_bist320 wrote:

So I have a fasta file of all Illumina sequences that I am feeding cutadapt to trim adapters for my pair-end RNA-seq

cutadapt -q 10,10 -a "${adapter}" -o "${file1%_1.fastq}_1_trimmed.fastq" -p "${file2%_2.fastq}_2_trimmed.fastq" "${file1}" "${file2}"

First, if my files are from CGHub/TCGA, does the '_1' and '_2" at the end denote a particular orientation that I should keep in mind when doing QC?

In cutadapt -a option is for forward adapter sequence and -A is for the reverse adapter sequence (for the paired file). I am wondering if cutadapt will know to reverse the adapters sequences I feed automatically or if I have to reverse the adapter sequences manually.

So like this 

cutadapt -q 10,10 -a "${adapter}" -A "${adapter}" -o "${file1%_1.fastq}_1_trimmed.fastq" -p "${file2%_2.fastq}_2_trimmed.fastq" "${file1}" "${file2}"
cutadapt rna-seq • 1.8k views
ADD COMMENTlink written 3.3 years ago by umn_bist320

_1 = R1 = Read 1

_2 = R2 = Read 2

ADD REPLYlink written 3.3 years ago by genomax67k

Right. But does it provide additional information other than read 1 and read 2? Ie, which one was sequenced in forward direction or reverse direction?

ADD REPLYlink written 3.3 years ago by umn_bist320

DNA is always sequenced in one direction 5'-->3'. You could consider R1 as forward and R2 as reverse, if that is how you want to think about the watson and crick strand.
 

ADD REPLYlink written 3.3 years ago by genomax67k
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