Missing chromosomal Information after sorting and deduplication step

Question

[tothepoint]

I am working on methylated data and found such issue where position is not mapped completely. May I know if someone encountered such data and how to fix. Here 2176 should be 2176X and this is all over the cromosome.

chr, start, end, strand

"1", 20850, 20850, "+"

"1", 20944, 20944, "+"

"1", 21128, 21128, "+"

"1", 2176, 2176, "+"

"1", 22386, 22386, "+"

Please share your views I will be grateful to you.

[GenoMax]

after sorting and deduplication step

What kind of sorting and deduplication? For BED files?

[tothepoint]

Respected Sir/Mam,

I received the data already preprocessed. The sorting and deduplication was performed on BAM file after QC and mapping. I found strange results and have no lead what could have happened and what leads to certain missing information.

[GenoMax]

How was the data posted above generated? What exactly do you mean by 2176 should be 2176x, as in a number is missing on the end?

[tothepoint]

Yes, a number is missing in the end. I checked in BAM file for one position and found the last digit was "0" which was missing. Similarly, there are many missing value. This output was generated by previous colleague and I have limited understanding. From the data I able to know this was methyl call as numCs and numTs column is reflecting some values.

Answer 1

[tothepoint]

There is an update in the following issue. I have contacted the developer and he found that within R these numbers were represented with scientific notation, like 2176+e1 for 2176_0_ or 2176+e2 for 2176_00_, and when we exported to bed/txt format the notation was not respected.