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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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FLASH: Low Percent Combined #37

Closed Transmystical closed 6 years ago

Transmystical commented 6 years ago

Greetings!

I have Illumina NextSeq500 150bp, paired end reads, generated from whole shotgun sequencing of environmental samples. These sequences have been quality filtered (Sickle, Phred > 20, default length to keep a read = 20bp). I am now trying to use FLASH to merge the paired end reads. For all of my metagenomes, I get really low numbers (as compared to the FLASH website and paper).

I ran the command as follows for all metagenomes: ./flash -M 150 -o Flash.out Forward.fastq Reverse.fastq | tee Flash.log

The range of Percent combined: Min = 13.04% ; Max = 52.72% ; Ave = 32.11%

I am curious as to why these numbers are so low or if this is considered to be "acceptable."

Many Thanks!!

lucapinello commented 6 years ago

Hi Transmystical, we don't provide support for FLASH in general since in CRISPResso it is used to merge overlapping reads from amplicon sequencing. So I would suggest you contact the authors of FLASH for your specific application.

Transmystical commented 6 years ago

Thank you!