XqKang commented 1 year ago

I am running nanocompore sampcomp and i got this:

Reading eventalign index files References found in index: 0 Filtering out references with low coverage References remaining after reference coverage filtering: 0

The script i am running is:

!/bin/bash

SBATCH --nodes=1

SBATCH --time=23:59:59

SBATCH --job-name=nanopolish_HelaDirect1

SBATCH --mem=100Gb

SBATCH --output=Output_nanocompore_SampComp.out

SBATCH -p short

module load minimap2/2.17 module load samtools/1.10 module load anaconda3/3.7 source activate /home/kang.xin/.conda/envs/nanocompore nanocompore sampcomp \ --file_list1 /work/rouhanifardlab/Xinqi/Data_guppy_6.3.2/Nanocompore/PSMB2_20230308_Trub1KD_R9_6.3.2_rna_hac_prom_eventcollapsed/out_eventalign_collapse.tsv \ --file_list2 /work/rouhanifardlab/Xinqi/Data_guppy_6.3.2/Nanocompore/PSMB2_HeLa_Direct1_6.3.2_eventcollapse/out_eventalign_collapse.tsv \ --label1 Trub1_KD \ --label2 HeLa_Direct1 \ --fasta /work/rouhanifardlab/Amr/Synthetic/Direct/SignalPrep/GRCh38.p10.genome.fa \ --min_coverage 1 \ --min_ref_length 1 \ --overwrite \ --outpath ./resultsc

Two of my collapsed eventalign file is following

TRUB1 KD collapsed eventalign file

Hela Direct1 collapsed eventalign file out_sampcomp.log I have also attached the log file of sampcomp

Thanks for you help!

lmulroney commented 1 year ago

Hi @XqKang,

It looks like you aligned the data to the reference genome instead of the reference transcriptome as we highly recommend when using Nanocompore. From what I can tell, the reference chromosomes are being discarded during the white listing step. I recommend redoing the pipeline from aligning to the transcriptome and then if you require the genome coordinates for your analysis, including a matched bed file to your transcriptome with the --bed option in sampcomp.

Let me know if this helps, Logan