pb-CpG-tools

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Criterion for error: Read sequence is too short for MM tag offsets in bam record

1

Dear developer! @ctsa I get five bam libraries in the same individual, but one of them has this error. To determine and resolve this error, I want to know the...

aewrwdw

genetic variants on CpG sites

3

Hi, I'm wondering how the genetic variants on CpG sites are treated by aligned_bam_to_cpg_scores. For example, when a diploid genome has a heterozygous SNP on a CpG site, how will...

qsonehara

Make bed file for reads processed by primrose

8

Hello, I am trying to find out the methylation status of haplotype-specific variants. These variants may not be assembled in the haploid genome (no mapping) and thus I need to...

oushujun

Is CpG status predicted at insertion variants?

4

Following a recent issue open in the IGV site (https://github.com/igvteam/igv/issues/1303), we wonder if `aligned_bam_to_cpg_scores.py` would call 5mC methylated CpG sites at insertions (i.e. at sites that are not in the...

elcortegano

Hi, as the title described, do you have a recommended ML threshold to judge the cytosine methylation is reliable.

leon945945

Hi, The output of pb-CpG-tools includes modification probability (column 4) and discretized modification probability (column 9) for each CpG site. I am wondering how should I consider using such information...

Jinyulin515

modsites-mode

3

I ran this code to use the modsites-mode aligned_bam_to_cpg_scores \ --bam ${f}haplotagged.bam \ --threads 8 \ --modsites-mode reference \ --ref /home/wdmays/coccolith_datasets/reference_genomes/Emihu2data/Emihu2_haploid_genome.fasta \ I am receiving this error: command-line setting: The...

wittney-m