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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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Explanation on the Epinano_Variants.py results #68

Closed yuxinPenny closed 3 years ago

yuxinPenny commented 3 years ago

Hi, I have successfully run the Epinano_Variants.py and got results. However, I found that in the output file, the X.ref column, which I expected to be the chromosome number (e.g. chr1), has values 0, 1, 2, ...6. Therefore, I cannot locate the each position.

I wonder what is the correct value for this column?

Below is my command: python3 /home/share/yuxin/EpiNano/Epinano_Variants.py -n 2 -R /home/share/yuxin/DATA/hg19.fa -b /home/share/yuxin/Nanopore/DATA/HEK_WT_Alignment_sorted.bam -s /home/share/yuxin/jvarkit/dist/sam2tsv.jar --type g

Huanle commented 3 years ago

Hi @yuxinPenny , There should not be X.ref column in the output. Insteadm there should be #Ref column in per.site.csv file. Maybe you have imported it into R? Can you double check and let me know? Can you also grep '>' hg19.fa and confirm the sequecnes IDs?