Yuk Kei Wan

Hi @Peng-Lingwei, You will have to add the following to your `config.yml` file: ``` criteria: readcount_min: ``` You can find more information about the config.yml file from here: https://xpore.readthedocs.io/en/latest/configuration.html Thanks!...

Hi @bhargava-morampalli, If you use prefiltering like indicated below, then `xpore diffmod` only outputs the significants positions according to the threshold: ``` notes: Pairwise comparison without replicates with default parameter...

Hi @Annie-GW, thanks for showing the log of the mapping to genome (using gene id and genome coordinates)! To map to transcriptome (using transcript id and transcriptome coordinates) you don't...

Hi Annie, which reference fasta and annotation gtf are you using? I'm not sure whether non-ensembl references and annotations could cause the problem. There are several things helpful to check...

Hi @6ge6, sorry for the delayed reply! I think I know where the problem is now: Here is a line from the Arabidopsis `gtf` file (`transcript_id "AT1G01010.1"`): ``` 1 araport11...

Hi @6ge6, thank you for waiting! I have updated [the xpore implementation on my fork](https://github.com/yuukiiwa/xpore), which is now compatible with Arabidopsis and Human Ensembl references. It is now pull requesting...

Hi @sunsetyerin, You will have to do transcriptome alignment with nanopolish. We suggest using the ENSEMBL fasta and gtf files. ENSEMBL human cDNA fasta: http://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz ENSEMBL human gtf: http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz Thanks!...

Hi @ynren1020, Currently, `xpore diffmod` is having trouble running with the `--save_models` parameters, so we would suggest you not include the `--save_models` parameters when running `xpore diffmod` as the `--save_models`...

Hi @zzf77, To distinguish which group having a higher m6A level in a single m6A motif, you can look into the `diff_mod_rate__vs_`, `z_score__vs_`, and `pval__vs_` columns. The direction (either negative...

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...