cutadapt cut the whole sequence from RNASeq fastq file

Question

[ddzhangzz]

One of sequences in my RNASeq fastq file looks like:

@7001458:226:C989WANXX:3:1102:17546:38724 1:N:0:CGATGT
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACAAAAAAATAAGCAGAGTTGTCAAAGTAAAAACAAAACAAAAAATAATAAGAA
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/<7////7/</</<///7///7//////7//7/7//77///////7///////

Because they were paired end, I cut adapters using cutadapt such like:

$cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
        -A AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT \
    -o $out1 -p $out2 \
    $input1 $input2

And the output showed the full sequence has been cut out:

@7001458:226:C989WANXX:3:1102:17546:38724 1:N:0:CGATGT

+

There does have the adatper sequence (GATCGGAAGAGCACACGTCTGAACTCCAGTCAC) in the RNASeq sequence but why the whole sequence has been removed to empty.

Answer 1

[Brian Bushnell]

The read started with the adapter. So, it was an adapter-dimer and the whole thing was trimmed since there were no genomic bases. The stuff after the adapter is just noise.

[ddzhangzz]

why? if manually remove the adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCAC from the seq, the trimmed should be CGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACAAAAAAATAAGCAGAGTTGTCAAAGTAAAAACAAAACAAAAAATAATAAGAA?

[Brian Bushnell]

Adapter:

AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

Read:

GATCGGAAGAGCACACGTCTGAACTCCAGTCAC CGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAA AAAACAAAAAAATAAGCAGAGTTGTC AAAGTAAAAACAAAACAAAAAATAATAAGAA

The part in bold is adapter. When adapter trimming, you trim the adapter and everything to the right. In this case, that's everything. The stuff to the right of the adapter sequence is not genomic.

[ddzhangzz]

Thanks! What do you mean not genomic? How do you know that?