gsukrit

Nanopolish Eventalign

1

Hi, I would like to know if the command _nanopolish eventalign_ changes the file size/content of the sequencing_summary file we specify in the command. If so, why? Since we are...

Error getting group name size

4

Hi, I was trying out the nanopolish index which consistently gave me the error as follows: [readdb] indexing /DATA/BioLab/Sukriti/PF_FAS70460_IIT/ACD_pass_FAST5/barcode02/ error getting group name size I had barcoded 3 samples in...

Error: Single positional indexer is out of bounds error

1

Hi, I tried to run this tool for some DRS Nanopore reads. However, the last command (m6anet inference) didn't execute and throws the following error:  If you can, please...

transcript_position column header from data.site_proba.csv output file

1

Hi team, I would like to have clarity on the column header _transcript_position_ in the output file of _data.site_proba.csv__ generated after the command _m6anet inference_. Does it indicate the position...

Understanding of the read-level prediction file output

1

If we wish to get the read level information of the methylated transcript, can we use the second column i.e. read levele and k-mer probability of the middle A of...

Column header _position_ in site_level_prediction

6

Hi team, I would like to have clarity on the column header position in the output file of site_level_prediction (CHEUI solo outputs). Does it indicate the position of modified base...

CHEUI model 2: prediction of stoichiometry and modification probability at transcriptomic sites : Executed with Error

5

Hi team, I was trying to run the command: python3 ../scripts/CHEUI_predict_model2.py -i read_level_m6A_predictions_sorted.txt -m ../CHEUI_trained_models/CHEUI_m6A_model2.h5 -o site_level_m6A_predictions.txt The command got executed, and the site-level file was made, but it also...

Setting up a suitable value for --filter-threshold or --percentile for modkit pileup command

5

Hi Team, I basecalled my data using Dorado in Super accuracy mode for 5mC and 5hmC in CG and 6mA all context and aligned with the reference genome during basecalling....