Length of sequence and qualities differ

[王程扬]

Dear Professor Zhang,

Happy Thanksgiving! I am writing to ask how to deal with error "Length of sequence and qualities differ" when I run cutadapt on reformatted eCLIP Read2? Below is the modified fastq as you suggested in https://zhanglab.c2b2.columbia.edu/index.php/ECLIP_data_analysis_using_CTK

@SN1001:449:HGTN3ADXX:1:1101:1046:1930 2:N:0:2

CCGCCATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCGTCCCG

+

FFFFFFFFIIFFIIFFFFIIII<BBFFFI7BBFB<B'07'0077''

The length of qualities indeed 5 bases less than the sequence... 

Thank you! 

for f in HepG2.RBFOX2.rep1.R2 HepG2.RBFOX2.rep2.R2 HepG2.RBFOX2_mock_input.rep1.R2

do

cutadapt  --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 5 -m 20 \

-a ATTGCTTAGATCGGAAGAGCGTCGTGT -a ACAAGCCAGATCGGAAGAGCGTCGTGT -a AACTTGTAGATCGGAAGAGCGTCGTGT -a AGGACCAAGATCGGAAGAGCGTCGTGT \

-a ANNNNGGTCATAGATCGGAAGAGCGTCGTGT -a ANNNNACAGGAAGATCGGAAGAGCGTCGTGT -a ANNNNAAGCTGAGATCGGAAGAGCGTCGTGT -a ANNNNGTATCCAGATCGGAAGAGCGTCGTGT \

-o $f.trim.fastq.gz ../fastq/$f.reformat.fastq > $f.cutadpt.log

done

[Chaolin Zhang]

The description here is a bit inaccurate here - Thanks for catching this!  

When you add the barcode to the sequence line, you will also need to modify the quality line accordingly (you can add some artificial scores here, e.g., 5 x I here).

I have fixed our documentation now.

Chaolin

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[王程扬]

Hi Professor Zhang,

Thank you very much for your prompt reply! 

Best,

Chengyang