Hello! I typically use PEAR to merge my two overlapping paired-end reads for one high quality read (R1 and R2 completely overlap). However, Galaxy not longer has the PEAR tool. What would be a good alternative?
Thanks, I tried FLASH but got an error message. Also tried fastq-join and got error also. My insert is 101 bp sequenced at 2x150 PE. Trimmed adapters, leaving ~100 bases of insert for R1 and ~ 100 bases for R2. Parameters used in FLASH was minimum overlap of 60 and max overlap of 100. Perhaps parameters were off?
Thanks, here's the error: Fatal error: Exit code 1 () [FLASH] ERROR: Input files do not contain the same number of reads Trimming likely have slightly changed number R1 and R2. Will try merging before trimming. For PE merge, I'd like the highest quality of reads (as PEAR usually gives) in order to minimize sequencing error through my unique molecular identifier. It's already difficult to resolve true UMI networks even with the allowance for 1-2 hamming distances.
