Clarification about filter_samples_by_positions.py

[pterzian]

Hi Peng,

So I am ready to train a model using samples extracted and labelled from bisulfite high confidence sites. I figured that the filter_samples_by_positions.py script was intented for this purpose. However some basic clarifications would be great :

• Because there is a --label argument, could you confirme I should use the script twice, one to extract and label methylated samples and one for unmethylated samples ?

• I see the position file should include only the chromosome and the genomic position (chromosome\tpos_in_forward_strand). Does it mean I also have to run this script twice to extract sample matching forward and reverse strand.

So I should build 4 lists of positions, two for the forward strand (methylated and unmethylated) and two for the reverse strand, then combine the outputs and shuffle it ?

Best,

Paul

[PengNi]

Hi Paul,

1. Yes, there should two position files, one for methylated samples, one for unmethylated samples.

2. there is no need to run twice for forward and reverse strand. The formart is as: chrom\tpos_in_forward_strand\tstrand, like:chr1\t2\t+ or chr1\t3\t-

So 2 position files should be build, one for methylated samples and one for unmethylated samples.

Best, Peng