pinellolab
larger amplicon analysis
Is your feature request related to a problem? Please describe. I would like to be able to run CRISPResso2 on amplicon ranging from 1,000 - 2,000 bp
Hi @weiss480
How long are your reads? Are you doing amplicon sequencing across the whole 1000-2000bp or are you sequencing fragments of the 1000-200bp region?
I am sequencing nanopore reads that are between 1000-2000 bp. I want to sequence across the whole read
On Mon, Apr 25, 2022 at 3:25 PM Kendell Clement @.***> wrote:
Hi @weiss480 https://github.com/weiss480
How long are your reads? Are you doing amplicon sequencing across the whole 1000-2000bp or are you sequencing fragments of the 1000-200bp region?
— Reply to this email directly, view it on GitHub https://github.com/pinellolab/CRISPResso2/issues/215#issuecomment-1109005950, or unsubscribe https://github.com/notifications/unsubscribe-auth/AURCY5A3IG6MYGBS2NP3QFDVG35SNANCNFSM5UJQXDPA . You are receiving this because you were mentioned.Message ID: @.***>
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Trevor Weiss
PhD Candidate
Department of Plant and Microbial Biology
Zhang Laboratory http://zhanglabumn.net
Centers for Genome Engineering https://cge.umn.edu and Precision Plant Genomics https://cppg.umn.edu
Phone: (515) 509 0193
Hi,
I tried to run CRISPResso2 for Pacbio amplicon sequencing reads around 3K.
This was my command: CRISPResso -r1 Z-H.0_0.fastq.gz -a TCACTGACTAACCCCGGAACCACACAGCTTCCCGTTCTCAGCTCCACAAACTTGGTGCCAAATTCTTCTCCCCTGGGAAGCATCCCTGGACACTTCCCAAAGGACCCCAGTCACTCCAGCCTGTTGGCTGCCGCTCACTTTGATGTCTGCAGGCCAGATGAGGGCTCCAGATGGCACATTGTCAGAGGGACACACTGTGGCCCCTGTGCCCAGCCCTGGGCTCTCTGTACATGAAGCAACTCCAGTCCCAAATATGTAGCTGTTTGGGAGGTCAGAAATAGGGGGTCCAGGAGCAAACTCCCCCCACCCCCTTTCCAAAGCCCATTCCCTCTTTAGCCAGAGCCGGGGTGTGCAGACGGCAGTCACTAGGGGGCGCTCGGCCACCACAGGGAAGCTGGGTGAATGGAGCGAGCAGCGTCTTCGAGAGTGAGGACGTGTGTGTCTGTGTGGGTGAGTGAGTGTGTGCGTGTGGGGTTGAGGGTGTTGGAGCGGGGAGAAGGCCAGGGGTCACTCCAGGATTCCAATAGATCTGTGTGTCCCTCTCCCCACCCGTCCCTGTCCGGCTCTCCGCCTTCCCCTGCCCCCTTCAATATTCCTAGCAAAGAGGGAACGGCTCTCAGGCCCTGTCCGCACGTAACCTCACTTTCCTGCTCCCTCCTCGCCAATGCCCCGCGGGCGCGTGTCTCTGGACAGAGTTTCCGGGGGCGGATGGGTAATTTTCAGGCTGTGAACCTTGGTGGGGGTCGAGCTTCCCCTTCATTGCGGCGGGCTGCGGGCCAGGCTTCACTGAGCGTCCGCAGAGCCCGGGCCCGAGCCGCGTGTGGAAGGGCTGAGGCTCGCCTGTCCCCGCCCCCCGGGGCGGGCCGGGGGCGGGGTCCCGGCGGGGCGGAGCCATGCGCCCCCCCCTTTTTTTTTTAAAAGTCGGCTGGTAGCGGGGAGGATCGCGGAGGCTTGGGGCAGCCGGGTAGCTCGGAGGTCGTGGCGCTGGGGGCTAGCACCAGCGCTCTGTCGGGAGGCGCAGCGGTTAGGTGGACCGGTCAGCGGACTCACCGGCCAGGGCGCTCGGTGCTGGAATTTGATATTCATTGATCCGGGTTTTATCCCTCTTCTTTTTTCTTAAACATTTTTTTTTAAAACTGTATTGTTTCTCGTTTTAATTTATTTTTGCTTGCCATTCCCCACTTGAATCGGGCCGACGGCTTGGGGAGATTGCTCTACTTCCCCAAATCACTGTGGATTTTGGAAACCAGCAGAAAGAGGAAAGAGGTAGCAAGAGCTCCAGAGAGAAGTCGAGGAAGAGAGAGACGGGGTCAGAGAGAGCGCGCGGGCGTGCGAGCAGCGAAAGCGACAGGGGCAAAGTGAGTGACCTGCTTTTGGGGGTGACCGCCGGAGCGCGGCGTGAGCCCTCCCCCTTGGGATCCCGCAGCTGACCAGTCGCGCTGACGGACAGACAGACAGACACCGCCCCCAGCCCCAGCTACCACCTCCTCCCCGGCCGGCGGCGGACAGTGGACGCGGCGGCGAGCCGCGGGCAGGGGCCGGAGCCCGCGCCCGGAGGCGGGGTGGAGGGGGTCGGGGCTCGCGGCGTCGCACTGAAACTTTTCGTCCAACTTCTGGGCTGTTCTCGCTTCGGAGGAGCCGTGGTCCGCGCGGGGGAAGCCGAGCCGAGCGGAGCCGCGAGAAGTGCTAGCTCGGGCCGGGAGGAGCCGCAGCCGGAGGAGGGGGAGGAGGAAGAAGAGAAGGAAGAGGAGAGGGGGCCGCAGTGGCGACTCGGCGCTCGGAAGCCGGGCTCATGGACGGGTGAGGCGGCGGTGTGCGCAGACAGTGCTCCAGCCGCGCGCGCTCCCCAGGCCCTGGCCCGGGCCTCGGGCCGGGGAGGAAGAGTAGCTCGCCGAGGCGCCGAGGAGAGCGGGCCGCCCCACAGCCCGAGCCGGAGAGGGAGCGCGAGCCGCGCCGGCCCCGGTCGGGCCTCCGAAACCATGAACTTTCTGCTGTCTTGGGTGCATTGGAGCCTTGCCTTGCTGCTCTACCTCCACCATGCCAAGGTAAGCGGTCGTGCCCTGCTGGCGCCGCGGGCCGCTGCGAGCGCCTCTCCCGGCTGGGGACGTGCGTGCGAGCGCGCGCGTGGGGGCTCCGTGCCCCACGCGGGTCCATGGGCACCAGGCGTGCGGCGTCCCCCTCTGTCGTCTTAGGTGCAGGGGGAGGGGGCGCGCGCGCTAGGTGGGAGGGTACCCGGAGAGAGGCTCACCGCCCACGCGGGCCCTGCCCACCCACCGGAGTCACCGCACGTACGATCTGGGCCGACCAGCCGAGGGCGGGAGCCGGAGGAGGAGGCCGAGGGGGCTGGGCTTGCGTTGCCGCTGCCGGCTGAAGTTTGCTCCCGGCCGCTGGTCCCGGACGAACTGGAAGTCTGAGCAGCGGGGGCGGGAGCCAGAGACCAGTGGGCAGGGGGTGCTCGGACCTTGGACCGCGGGAGGGCAGAGAGCGTGGAGGGGGCAGGGCGCAGGAGGGAGAGGGGGCTTGCTGTCACTGCCACTCGGTCTCTTCAGCCCTCGCCGCGAGTTTGGGAAAAGTTTTGGGGTGGATTGCTGCGGGGACCCCCCCTCCCTGCTGGGCCACCTGCGCCGCGCCAACCCCGCCCGTCCCCGCTCGCGTCCCGCTCGGTGCCCGCCCTCCCCCGCCCGGCCGGGTGCGCGCGGCGCGGAGCCGATTACATCAGCCCGGGCCTGGCCGGCCGCGTGTTCCCGGAGCCTCGGCTGCCCGAATGGGGAGCCCAGAGTGGCGAGCGGCACCCCTCCCCCCGCCAGCCCTCCGCGGGAAGGTGACCTCTCGAGGTAGCCCCAGCCCGGGGATCCAGAGAACCATCCCTACCCCTTCCTACTGTCTCCAGACCCTACCTCTGCCCAGTGCTAGGAGGAATTTCCTGACGCCCCTTCTCTTCACCCATTTCCTTTTTAGCCTGGAGAGAAGCCCCTGTCACCCCGCTTATTTTCATTTCTCTCTGCGGAGAAGATCCATCTAACCCCTTTCTGGCCCCAGAGTCCAGGGAAAGGATGATCACTGTCAGAAGTCGTGGC --prime_editing_override_prime_edited_ref_seq TCACTGACTAACCCCGGAACCACACAGCTTCCCGTTCTCAGCTCCACAAACTTGGTGCCAAATTCTTCTCCCCTGGGAAGCATCCCTGGACACTTCCCAAAGGACCCCAGTCACTCCAGCCTGTTGGCTGCCGCTCACTTTGATGTCTGCAGGCCAGATGAGGGCTCCAGATGGCACATTGTCAGAGGGACACACTGTGGCCCCTGTGCCCAGCCCTGGGCTCTCTGTACATGAAGCAACTCCAGTCCCAAATATGTAGCTGTTTGGGAGGTCAGAAATAGGGGGTCCAGGAGCAAACTCCCCCCACCCCCTTTCCAAAGCCCATTCCCTCTTTAGCCAGAGCCGGGGTGTGCAGACGGCAGTCACTAGGGGGCGCTCGGCCACCACAGGGAAGCTGGGTGAATGGAGCGAGCAGCGTCTTCGAGAGTGAGGACGTGTGTGTCTGTGTGGGTGAGTGAGTGTGTGCGTGTGGGGTTGAGGGTGTTGGAGCGGGGAGAAGGCCAGGGGTCACTCAGTAACCCGGAGCTCTAATAGCCAGAGCCGGGGTGTGCAGACGGCAGTCACTAGGGGGCGCTCGGCCACCACAGGGAAGCTGGGTGAATGGAGCGAGCAGCGTCTTCGAGAGTGAGGACGTGTGTGTCTGTGTGGGTGAGTGAGTGTGTGCGTGTGGGGTTGAGGGTGTTGGAGCGGGGAGAAGGCCAGGGGTCACTCCAGGATTCCAATAGATCTGTGTGTCCCTCTCCCCACCCGTCCCTGTCCGGCTCTCCGCCTTCCCCTGCCCCCTTCAATATTCCTAGCAAAGAGGGAACGGCTCTCAGGCCCTGTCCGCACGTAACCTCACTTTCCTGCTCCCTCCTCGCCAATGCCCCGCGGGCGCGTGTCTCTGGACAGAGTTTCCGGGGGCGGATGGGTAATTTTCAGGCTGTGAACCTTGGTGGGGGTCGAGCTTCCCCTTCATTGCGGCGGGCTGCGGGCCAGGCTTCACTGAGCGTCCGCAGAGCCCGGGCCCGAGCCGCGTGTGGAAGGGCTGAGGCTCGCCTGTCCCCGCCCCCCGGGGCGGGCCGGGGGCGGGGTCCCGGCGGGGCGGAGCCATGCGCCCCCCCCTTTTTTTTTTAAAAGTCGGCTGGTAGCGGGGAGGATCGCGGAGGCTTGGGGCAGCCGGGTAGCTCGGAGGTCGTGGCGCTGGGGGCTAGCACCAGCGCTCTGTCGGGAGGCGCAGCGGTTAGGTGGACCGGTCAGCGGACTCACCGGCCAGGGCGCTCGGTGCTGGAATTTGATATTCATTGATCCGGGTTTTATCCCTCTTCTTTTTTCTTAAACATTTTTTTTTAAAACTGTATTGTTTCTCGTTTTAATTTATTTTTGCTTGCCATTCCCCACTTGAATCGGGCCGACGGCTTGGGGAGATTGCTCTACTTCCCCAAATCACTGTGGATTTTGGAAACCAGCAGAAAGAGGAAAGAGGTAGCAAGAGCTCCAGAGAGAAGTCGAGGAAGAGAGAGACGGGGTCAGAGAGAGCGCGCGGGCGTGCGAGCAGCGAAAGCGACAGGGGCAAAGTGAGTGACCTGCTTTTGGGGGTGACCGCCGGAGCGCGGCGTGAGCCCTCCCCCTTGGGATCCCGCAGCTGACCAGTCGCGCTGACGGACAGACAGACAGACACCGCCCCCAGCCCCAGCTACCACCTCCTCCCCGGCCGGCGGCGGACAGTGGACGCGGCGGCGAGCCGCGGGCAGGGGCCGGAGCCCGCGCCCGGAGGCGGGGTGGAGGGGGTCGGGGCTCGCGGCGTCGCACTGAAACTTTTCGTCCAACTTCTGGGCTGTTCTCGCTTCGGAGGAGCCGTGGTCCGCGCGGGGGAAGCCGAGCCGAGCGGAGCCGCGAGAAGTGCTAGCTCGGGCCGGGAGGAGCCGCAGCCGGAGGAGGGGGAGGAGGAAGAAGAGAAGGAAGAGGAGAGGGGGCCGCAGTGGCGACTCGGCGCTCGGAAGCCGGGCTCATGGACGGGTGAGGCGGCGGTGTGCGCAGACAGTGCTCCAGCCGCGCGCGCTCCCCAGGCCCTGGCCCGGGCCTCGGGCCGGGGAGGAAGAGTAGCTCGCCGAGGCGCCGAGGAGAGCGGGCCGCCCCACAGCCCGAGCCGGAGAGGGAGCGCGAGCCGCGCCGGCCCCGGTCGGGCCTCCGAAACCATGAACTTTCTGCTGTCTTGGGTGCATTGGAGCCTTGCCTTGCTGCTCTACCTCCACCATGCCAAGGTAAGCGGTCGTGCCCTGCTGGCGCCGCGGGCCGCTGCGAGCGCCTCTCCCGGCTGGGGACGTGCGTGCGAGCGCGCGCGTGGGGGCTCCGTGCCCCACGCGGGTCCATGGGCACCAGGCGTGCGGCGTCCCCCTCTGTCGTCTTAGGTGCAGGGGGAGGGGGCGCGCGCGCTAGGTGGGAGGGTACCCGGAGAGAGGCTCACCGCCCACGCGGGCCCTGCCCACCCACCGGAGTCACCGCACGTACGATCTGGGCCGACCAGCCGAGGGCGGGAGCCGGAGGAGGAGGCCGAGGGGGCTGGGCTTGCGTTGCCGCTGCCGGCTGAAGTTTGCTCCCGGCCGCTGGTCCCGGACGAACTGGAAGTCTGAGCAGCGGGGGCGGGAGCCAGAGACCAGTGGGCAGGGGGTGCTCGGACCTTGGACCGCGGGAGGGCAGAGAGCGTGGAGGGGGCAGGGCGCAGGAGGGAGAGGGGGCTTGCTGTCACTGCCACTCGGTCTCTTCAGCCCTCGCCGCGAGTTTGGGAAAAGTTTTGGGGTGGATTGCTGCGGGGACCCCCCCTCCCTGCTGGGCCACCTGCGCCGCGCCAACCCCGCCCGTCCCCGCTCGCGTCCCGCTCGGTGCCCGCCCTCCCCCGCCCGGCCGGGTGCGCGCGGCGCGGAGCCGATTACATCAGCCCGGGCCTGGCCGGCCGCGTGTTCCCGGAGCCTCGGCTGCCCGAATGGGGAGCCCAGAGTGGCGAGCGGCACCCCTCCCCCCGCCAGCCCTCCGCGGGAAGGTGACCTCTCGAGGTAGCCCCAGCCCGGGGATCCAGAGAACCATCCCTACCCCTTCCTACTGTCTCCAGACCCTACCTCTGCCCAGTGCTAGGAGGAATTTCCTGACGCCCCTTCTCTTCACCCATTTCCTTTTTAGCCTGGAGAGAAGCCCCTGTCACCCCGCTTATTTTCATTTCTCTCTGCGGAGAAGATCCATCTAACCCCTTTCTGGCCCCAGAGTCCAGGGAAAGGATGATCACTGTCAGAAGTCGTGGC -o Z-H.0_0_results_1 --debug
But I encountered this error:
CRITICAL @ Tue, 17 May 2022 21:42:22: Traceback (most recent call last): File "/home/pan/miniconda3/lib/python3.9/site-packages/CRISPResso2/CRISPRessoCORE.py", line 1947, in main aln_stats = process_fastq(processed_output_filename, variantCache, ref_names, refs, args) File "/home/pan/miniconda3/lib/python3.9/site-packages/CRISPResso2/CRISPRessoCORE.py", line 442, in process_fastq new_variant = get_new_variant_object(args, fastq_seq, refs, ref_names, aln_matrix, pe_scaffold_dna_info) File "/home/pan/miniconda3/lib/python3.9/site-packages/CRISPResso2/CRISPRessoCORE.py", line 228, in get_new_variant_object fws1, fws2, fwscore=CRISPResso2Align.global_align(fastq_seq, refs[ref_name]['sequence'], matrix=aln_matrix, gap_incentive=refs[ref_name]['gap_incentive'], gap_open=args.needleman_wunsch_gap_open, gap_extend=args.needleman_wunsch_gap_extend,) File "CRISPResso2/CRISPResso2Align.pyx", line 382, in CRISPResso2.CRISPResso2Align.global_align Exception: ('wtf4!:pointer: %i', 0)
CRITICAL @ Tue, 17 May 2022 21:42:22: Unexpected error, please check your input.
ERROR: ('wtf4!:pointer: %i', 0)
I don't know if CRISPResso2 could be used for long amplicon.
I suspect that this is happening because the alignment is requiring too much memory. Do you happen to know how much RAM your computer has?
We're closing this issue because it hasn't been updated recently. If this issue still exists, please reopen this issue and we'll look into it!
Hello, I see that this thread was closed with no actual answear. I will try to ask again:
Is it possible to use CRISPReso2 for long amplicons (~4000 bp) with long read sequencing (ONT)?
