Question: PEAR alternative for merging overlapping paired-end reads using Galaxy tools
0
gravatar for mlhoang3
7 weeks ago by
mlhoang30
United States
mlhoang30 wrote:

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?

galaxy • 160 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by mlhoang30
0
gravatar for Devon Ryan
7 weeks ago by
Devon Ryan1.8k
Germany
Devon Ryan1.8k wrote:

You can use the FLASH tool.

ADD COMMENTlink written 7 weeks ago by Devon Ryan1.8k
0
gravatar for mlhoang3
7 weeks ago by
mlhoang30
United States
mlhoang30 wrote:

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?

ADD COMMENTlink written 7 weeks ago by mlhoang30

You'd need to post the error message. I'm curious what you expect to gain from merging reads if they're all expected to be complete overlaps. I would think it'd be simpler to take read 1 and be done with it.

ADD REPLYlink written 7 weeks ago by Devon Ryan1.8k
0
gravatar for mlhoang3
7 weeks ago by
mlhoang30
United States
mlhoang30 wrote:

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.

ADD COMMENTlink written 7 weeks ago by mlhoang30

Make sure to do trimming on both files at the same time with a tool like trimmomatic or trim galore. Trimming the mates independently will cause problems like this.

ADD REPLYlink written 7 weeks ago by Devon Ryan1.8k
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