"Alleles_frequency_table_around_sgRNA_GTTTTCTCGCACTTAAGCTC.txt" output question

[weiss480]

I am trying to get the output file "Alleles_frequency_table_around_sgRNA_GTTTTCTCGCACTTAAGCTC.txt" to only show the protospacer and PAM sequence in the Aligned_Sequence and Reference_Sequence columns. Is this something that can be done using your CRISPResso software?

[kclem]

Hi @weiss480,

Thanks for using CRISPResso.

The plotting window currently extends on both sides of the predicted cut site because we thought that users would be interested in results centered at this position (the position of action).

I just added a script (947fbab) plotCustomAllelePlot.py. Download this script to your working directory. Run CRISPResso with the parameter --write_detailed_allele_table. After the run is complete, you can run this script and adjust the plotting positions.

For example, if your finished folder is 'CRISPResso_on_finished_run' and you want your output files to be called 'mod_plot.pdf', run:

python plotCustomAllelePlot.py -f CRISPResso_on_finished_run -o mod_plots --plot_left 20 --plot_right 3

This will produce a plot where 20bp to the left of the cut site and 3bp to the right of the cut site is plotted.

If you run into any problems, let me know.

[weiss480]

Hey, thanks for the quick reply. I am having issues running this. After running CRISPResso2 with the parameter --write_detailed_allele_table I entered the following (below) into the terminal. CRISPResso_on_5907-8 is inside the folder 86B_TEST. Any advice? Thanks a ton!

(base) trevorweiss@Trevors-MacBook-Air ~ % cd /Volumes/Backup_Plus/School/Sequencing/051121_NGS_86B_T2_AZA_treatment_and_controls/30-522520824/00_fastq

(base) trevorweiss@Trevors-MacBook-Air 00_fastq % ls

10_R1_001.fastq.gz

10_R2_001.fastq.gz

11_R1_001.fastq.gz

11_R2_001.fastq.gz

12_R1_001.fastq.gz

12_R2_001.fastq.gz

13_R1_001.fastq.gz

13_R2_001.fastq.gz

14_R1_001.fastq.gz

14_R2_001.fastq.gz

15_R1_001.fastq.gz

15_R2_001.fastq.gz

16_R1_001.fastq.gz

16_R2_001.fastq.gz

17_R1_001.fastq.gz

17_R2_001.fastq.gz

18_R1_001.fastq.gz

18_R2_001.fastq.gz

1_R1_001.fastq.gz

1_R2_001.fastq

1_R2_001.fastq.gz

2_R1_001.fastq.gz

2_R2_001.fastq.gz

3_R1_001.fastq.gz

3_R2_001.fastq.gz

4_R1_001.fastq.gz

4_R2_001.fastq.gz

5_R1_001.fastq.gz

5_R2_001.fastq.gz

6_R1_001.fastq.gz

6_R2_001.fastq.gz

7_R1_001.fastq.gz

7_R2_001.fastq.gz

86B_TEST

8_R1_001.fastq.gz

8_R2_001.fastq.gz

9_R1_001.fastq.gz

9_R2_001.fastq.gz

Seed_ID_K_86B_T2_AZA_treatment_p2wA6_insertions_and_deletions

Seed_ID_P_86B_T2_AZA_treatment_p1wC4_insertions_and_deletions

Seed_ID_W_86B_T2_AZA_treatment_p3wC4_insertions_and_deletions

Seed_ID_X_86B_T2_AZA_NON-treatment_control_p1wB4_insertions_and_deletions

Seed_ID_Y_86B_T2_AZA_NON-treatment_control_p1wB5_insertions_and_deletions

Seed_ID_Z_86B_T2_AZA_NON-treatment_control_p1wC2_insertions_and_deletions

md5sum_list.txt

plotCustomAllelePlot.py

(base) trevorweiss@Trevors-MacBook-Air 00_fastq % python plotCustomAllelePlot.py -f CRISPResso_on_5907-8 -o mod_plots --plot_left 20 --plot_right 3

Traceback (most recent call last):

File "/Volumes/Backup_Plus/School/Sequencing/051121_NGS_86B_T2_AZA_treatment_and_controls/30-522520824/00_fastq/plotCustomAllelePlot.py", line 12, in

from CRISPResso2 import CRISPRessoPlot

ModuleNotFoundError: No module named 'CRISPResso2'

(base) trevorweiss@Trevors-MacBook-Air 00_fastq %

On Sat, Jun 19, 2021 at 11:30 PM Kendell Clement @.***> wrote:

Closed #104 https://github.com/pinellolab/CRISPResso2/issues/104.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/pinellolab/CRISPResso2/issues/104#event-4913033195, or unsubscribe https://github.com/notifications/unsubscribe-auth/AURCY5EFLKT6EKGNY6FXL3DTTVVEPANCNFSM466RUBIA .

--

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

[kclem]

1) You have to load the crispresso2 conda environment before it will work. (that's the ModuleNotFoundError: No module named 'CRISPResso2' error) 2) CRISPResso produces a folder called 'CRISPResso_on_XXXX' and that folder name is the one you have to pass to this program. If that folder is inside of 86B_TEST you can pass this program the path to the CRISPResso_on_XXXX folder like this: python plotCustomAllelePlot.py -f 86B_TEST/CRISPResso_on_5907-8 -o mod_plots --plot_left 20 --plot_right 3