Closed strohmjeff closed 6 years ago
Hi 1) Regarding flash, yes you can run it before running CRISPResso with the options you like and then run CRISPResso on the merged file specifying a single file.
2) Looking at your reference and at few reads of your fastq file it seems the reference is too long.
The refererence is: TCTGCTTACTGCAACTCGCTCCGGCCGCTGGGCGTAGCTGCGACTCGGCGGAGTCCCGGCGGCGCGTCCTTGTTCTAACCCGGCGCGCCATGACCGTCGCGCGGCCGAGCGTGCCCGCGGCGCTGCCCCTCCTCGGGGAGCTGCCCCGGCTGCTGCTGCTGGTGCTGTTGTGCCTGCCGGCCGTGTGGGGTGAGTAGGGGCCCGGCGGCCGGGGAAGCCCCTGGGCTGGGTGGGAGGTCCAAGTCGGTCTCTGAGACACGCACAGGGGCCGGCGACTTGGCAGGTGGGGAGCTTGGCCCGCGGTCGTGGTTCCCGCCGTCCTGTGCCTTTAAGGCTCTCGCCGCTCACCAGCATTTGGGGCTCCTGCTGTGTCGGCCCCCAGCTGACTTGGCTTTAGGGGTCGGCGTGGAGGGTTAAAGAGGCCCCGGCTGGGTTTGCGGAGCAGCCAAGCCTGGCAAAATCGAAAGGGAGGGCTCAAAGAGACTGTATCCTTAACCCCCAAAAAGCTGGTCTAAAAGGATGGGAGGCCAGACCGCTGACCGTTCCCCACTCTCGACAGAGTCCAGCCGTGTGGAGCACACGATGCTGCAAACTTGCATGTCATCTCTTTCAGGTGTGGCATTTCAAGGGGGCTTGTGTCTTGAAAACAGCAACTGTGAGGACACTTGATAGTCATTTCCTTCAGTTCTGCTTTTGTCTCCCTAGGTGACTGTGGCCTTCCCCCAGATGTACCTAATGCCCAGCCAGCTTTGGAAGGCCGTACAAGTTTTCCCGAGGATACTGTAATAACGTACAAATGTGAAGAAAGCTTTGTGAAAATTCCTGGCGAGAAGGACTCAGTGATCTGCCTTAAGGGCAGTCAATGGTCAGATATTGAAGAGTTCTGCAATCGTAAGTTCTTCATCTTTTTAGAAAAGTTCTGGGAATGGAATGTATCTTAAATTTATTTTTATATACCTTTGGAGTGACTAGTAATTGATAGTTCTCTAGCGTTACTAAACCCCAGGGTATACCCTGTTGGCACGTCACACTC
One of the read is:
CAGATCACTGAGTCCTTCTCGCCAGGAATTTTCACAAAGCTTTCTTCACATTTGTACGTTATTACAGTATACAGTATAATAACTTGTACGGCCTCGGGAAAACTTGTACGGCCTTCCAAAGCTGGCTGGGCATTAGGTACATCTGGGGGAAGGCCACAGTCACCTAGGGAGACAAAAGCAGAACTGAAGGAAATGACTATCAAGTGTCCTCACAGTTGCTGTTTTCAAGACACAAGCCCCCTTGAAATGCCACACCTG
So something is wrong here, please double check the provided reference.
OK thanks, yes I didn't realize the reference had to only cover the active region. I was using the entire gene. Shortening it to the active region observed in GATK worked.
Thanks again
-Jeff
Hi Jeff, cool.
Closing this.
Hi there,
I am attempting your pipeline with single end reads (since my overlap is over 65bp and I get an error from flash when trying to merge. Is there any way to adjust flash params?). Reads were quality filtered and merged with usearch.
I have attached my merged reads and my reference sequence. They gave reasonable results with GATK/MuTect2...
I get this error, thanks for your help!: