Issue regarding the HEK293T data and preprocessed HEK293T data

[daewon-gong]

Hello,

I noticed some issues while trying to run xpore on 3 replicates of the HEK293T-Mettl3-KO data and 3 replicates of the HEK293T-WT data downloaded from the provided ENA website using aspera.

1. I get this gzip error while trying to untar HEK293T-WT-rep2, the 20190918_Sho_M3-2.tar.gz file in HEK293T-KO-rep3: gzip: 20190918_Sho_M3-2.tar.gz: invalid compressed data--crc error. I tried re-downloading multiple times and still get the same errors.

2. Giving the preprocessed HEK293T data a try which were downloaded from zenodo. Running xpore diffmod --config config_file didn't give any errors but gave empty results with a0 ids to be testing ... message in the beginning.

Could someone check on these files for us. Thank you!

FYI: @jts

[yuukiiwa]

Hi @daewon-gong,

1. Do you mind sending us the md5sum of the file you downloaded, please? We can then check whether the file from ENA is the same the file on our side or it is corrupted.
2. Do you mind providing us the config.yml file so that we can see what the issue is.

Thank you!

Best wishes, Yuk Kei

[daewon-gong]

Hi @yuukiiwa ,

1. Here are the md5sum of the files:

• 38dbbb5c3531a627c57110ad8c3b628f HEK293T-WT-rep2.tar.gz
• 94231007837505fddfc374714e112847 HEK293T-Mettl3-KO-rep3.tar.gz
• 3c85195505b5891752318580e41e28bc 20190918_Sho_M3-2.tar.gz (This one is the file that seems corrupted in HEK293T-Mettl3-KO-rep3.tar.gz)

2. This is the config file I used:

   
   data:
   KO:
       rep1: ./HEK293T_KO_rep1_pre/dataprep
       rep2: ./HEK293T_KO_rep2_pre/dataprep
       rep3: ./HEK293T_KO_rep3_pre/dataprep
   WT:
       rep1: ./HEK293T_WT_rep1_pre/dataprep
       rep2: ./HEK293T_WT_rep2_pre/dataprep
       rep3: ./HEK293T_WT_rep3_pre/dataprep

out: ./out

Thanks for the help!

Best,
Sean Gong

[rezarahman12]

Hi @yuukiiwa I have downloaded the preprocessed HEK293T-Mettl3-KO data and 3 replicates of the HEK293T-WT data from zenodo from your suggested links as given in other discussion threads (https://zenodo.org/record/5103099 and (https://zenodo.org/record/5101752). I unzipped the file using tar -xvzf file.tar.gz command and found all below files for each HEK293T-Mettl3-KO data and HEK293T-Mettl3-WT data -

data.index data.json data.log data.readcount eventalign.index transcript_id_version_merged.gtf

I ran xpore diffmod --config config_file as below

!/bin/bash

PBS -A UQ-QBI

PBS -l select=1:ncpus=10:mem=30GB

PBS -l walltime=10:00:00

PBS -N xpore_diffmod2

cd $PBS_O_WORKDIR module load xpore/2.1

xpore diffmod --config Hek293T_config2.yml

and obtained an error- "Using the signal of unmodified RNA from /sw/QFAB/miniconda3/envs/xpore_2.1/lib/python3.9/site-packages/xpore/diffmod/model_kmer.csv 0 ids to be testing ..."

My yml file is given below:

data: KO: rep1: /scratch/project_mnt/S0077/xPore/rawdata/HEK293T-METTL3-KO-rep1/new_argsort_dataprep_noNbug rep2: /scratch/project_mnt/S0077/xPore/rawdata/HEK293T-METTL3-KO-rep2/new_argsort_dataprep_noNbug rep3: /scratch/project_mnt/S0077/xPore/rawdata/HEK293T-METTL3-KO-rep3/new_argsort_dataprep_noNbug

WT: rep1: /scratch/project_mnt/S0077/xPore/rawdata/HEK293T-WT-rep1/new_argsort_dataprep rep2: /scratch/project_mnt/S0077/xPore/rawdata/HEK293T-WT-rep2/new_argsort_dataprep rep3: /scratch/project_mnt/S0077/xPore/rawdata/HEK293T-WT-rep3/new_argsort_dataprep

out: /scratch/project_mnt/S0077/xPore/rawdata/diffmod_out method: prefiltering: method: t-test threshold: 0.1

Could you please tell me how to get rid of the problem?

Best regards Reza