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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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Specify the FLASH --max-overlap parameter? #16

Closed martinaryee closed 7 years ago

martinaryee commented 7 years ago

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?

[FLASH]  
[FLASH] Read combination statistics:
[FLASH]     Total pairs:      2554170
[FLASH]     Combined pairs:   415920
[FLASH]     Uncombined pairs: 2138250
[FLASH]     Percent combined: 16.28%
[FLASH]  
[FLASH] Writing histogram files.
[FLASH] WARNING: An unexpectedly high proportion of combined pairs (10.04%)
overlapped by more than 100 bp, the --max-overlap (-M) parameter.  Consider
increasing this parameter.  (As-is, FLASH is penalizing overlaps longer than
100 bp when considering them for possible combining!)
lucapinello commented 7 years ago

Yes you can with --max_paired_end_reads_overlap. Please let me know if this fixes your problem.

martinaryee commented 7 years ago

Yes - The --max_paired_end_reads_overlap removes the FLASH warning and fixes the problem. Thanks!

lucapinello commented 7 years ago

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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asgiraldoc commented 5 years ago

Hey guys, I had the same problem and your solution didn't work for me :(