Comments (2)
Hi Charles,
It seems that in your experimental design you have a large amplicon of 464 bp but you can sequence only the ends of it since you are using 150bp PE.
Unfortunately you cannot use CRISPResso in this scenario since you cannot sequence the entire unmodified amplicon.
For paired end reads that means that any pair of reads should partially overlap. This is enforced since if you sequence only the ends of an amplicon you don't know what will happen inside and this will make the quantifications of indels wrong.
That is why FLASH is throwing this error since it is impossible to find any overlap for paired reads in your case.
Hope this is helpful
from crispresso.
Thanks. Yeah actually my case turned out my collaborators just gave me an amplicon sequence that was too long
from crispresso.
Related Issues (20)
- mutation frequency plot HOT 1
- Unexpected error: invalid literal for int() with base 10: '0rc1' HOT 10
- Error "'numpy.int64' HOT 7
- Front End Code HOT 4
- Use --min_identity_score for read vs amplicon HOT 3
- FLASH: Low Percent Combined HOT 2
- CRIPRessoPooled - query HOT 1
- free variable 'df_genes' referenced before assignment in enclosing scope", u'occurred at index Site1' HOT 7
- Run for a long times HOT 3
- Error while generating plots with Cpf1 data HOT 4
- [FLASH] ERROR: Maximum overlap (-173) cannot be less than the minimum overlap (4). HOT 1
- ERROR: The amplicons should be all distinct! HOT 1
- modify the python scripts for availability to other CRISPR systems HOT 1
- Left-aligning option HOT 7
- ERROR: Flash failed to run, please check the log file. HOT 1
- Appears to be counting reads with deletions as unedited HOT 1
- Last stage error Error with FLASH for CRISPRessoPooled.py HOT 5
- CRISPResso command failed (return value 127) on region #0: HOT 1
- Longer Allele Sequences HOT 4
- Alignment error, please check your input
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from crispresso.