Closed martinaryee closed 7 years ago
Yes you can with --max_paired_end_reads_overlap. Please let me know if this fixes your problem.
Yes - The --max_paired_end_reads_overlap
removes the FLASH warning and fixes the problem. Thanks!
Great!
On Apr 10, 2017 11:58 PM, "Martin Aryee" notifications@github.com wrote:
Yes - The --max_paired_end_reads_overlap removes the FLASH warning and fixes the problem. Thanks!
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Hey guys, I had the same problem and your solution didn't work for me :(
I get the following warning from FLASH about a high proportion of paired end reads overlapping by more than 100bp. This pooled dataset has many short amplicons and 150bp PE reads, so this is probably to be expected. Is it possible to specify the
--max-overlap (-M)
parameter to fix this?