Najeeb Ashraf Syed

Here is the first few lines of the data. > head(a) chromosome position base.ref depth.normal depth.tumor depth.ratio Af Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor 1 1 12817 N 3 20...

Thanks alot !! It works !! On Tue, Jun 2, 2020 at 5:29 AM stellaoh wrote: > I think this error resulted from "chromosome name" > > If you edit...

Hi team, It is taking forever to resolve the dependency. We tried another option, and it's not working also. Please check below error. File "/gpfs/software/genomics/CRISPRme/v2.0.9/bin/mamba", line 7, in from mamba.mamba...

Hi Now getting this error $ mamba create -n crisprme *python=3.8* crisprme -y Traceback (most recent call last): File "/gpfs/software/genomics/CRISPRme/v2.0.9/bin/mamba", line 7, in from mamba.mamba import main File "/gpfs/software/genomics/CRISPRme/v2.0.9/lib/python3.9/site-packages/mamba/mamba.py", line...

Hi Team, Finally !! Our IT was able to install the software. Please let us know if we can download the reference data used in this analysis. Can you please...

Dear Team, Thanks for your fantastic work! I was able to run and able to generate these files along with other files. final_results_sg1617.bestMerge.txt.bestCFD.txt.CTAACAGTTGCTTTTATCACNNN final_results_sg1617.bestMerge.txt.bestCRISTA.txt.CTAACAGTTGCTTTTATCACNNN final_results_sg1617.bestMerge.txt.bestmmblg.txt.CTAACAGTTGCTTTTATCACNNN Are these actual output files?...

Hi Manuel, crisprme.py complete-search --genome Genomes/hg38/ --vcf list_vcf.txt/ --guide sg1617.txt --pam PAMs/20bp-NGG-SpCas9.txt --annotation Annotations/encode+gencode.hg38.bed --samplesID list_samplesID.txt --be-window 4,8 --be-base A --gene_annotation Annotations/gencode.protein_coding.bed --bMax 2 --mm 6 --bDNA 2 --bRNA 2...

Dear team, Do you have some updates on this request? Thanks for your kind help and support !! Regards, Najeeb

Hi Manuel, I am still getting some errors. Please take a look at the attachment. [log_error_no_check.txt](https://github.com/pinellolab/CRISPRme/files/10830559/log_error_no_check.txt) I am running it like this. crisprme.py complete-search --genome Genomes/hg38/ --vcf list_vcf.txt --guide sg1617.txt...

Hi Team, I was able to generate the two files. I have noticed that my all_results_with_alternative_alignments.tsv file has only chrM results, how ever _integrated_results.tsv file has results from chr12, chr22,...