Empty output file after trim primers with Cutadapt
Dear all, I have a problem with Cutadapt. After trimming primers from R1 and R2 fastq files, output fastq file is empty. Only the name of read is conserved. Lines corresponding with quality and DNA sequence are removed on the output fastq file. Primers are placed in 3' end for both R1 and R2 reads and I used the -a option followed by the sequence of primers. Output fastq file is generated by it is incompleted. I tried first merging both reads and then trimming 3' and 5' adapters using -a and -g options, but this problem remain also when using the merge fastq file. Anyone could help me to fix this problem?
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