.. _collapse: *************** Collapse fastq(.gz) files *************** **Definition** Normally quality values are lost in small RNA-seq pipelines due to collapsing after adapter recognition. This option allow to collapse reads after adapter removal with ``cutadapt`` or any other tool. This way the mapping can use quality values, allowing to map using ``bwa`` for instance, or any other alignment tool that doesn't support FASTA files. **Methods** The new quality values are the average of each of the sequence collapse. **Example** :: seqcluster collapse -f sample_trimmed.fastq -o collapse * ``-f`` is the fastq(.gz) file * ``-o`` the folder where the outout will be created. A new FASTQ file, where the name stand for:: @seq_[0-9]_x[0-9] The number right after ``_x`` means the abundance of this sequence in the sample