cutadapt: forward and reverse adapter sequence options
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}"
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umn_bist •
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_1 = R1 = Read 1
_2 = R2 = Read 2
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?
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.