Why am I getting a rough/unsmooth hockey stick plot?

[acheng314159]

[acheng314159]

Here's the English translation of your explanation:

"I found part of the reason.

My narrowPeak files contained non-standard chromosome names like chr11_KI270721v1_random. When these lines were present, the files generated by ROSE were incomplete.

To remove these lines, I used a command like: awk -F'\t' 'BEGIN {OFS="\t"} $1 ~ /^chr([1-9]|1[0-9]|2[0-2]|X|Y|M)$/ {print $0}' "$filename" > "$temp_output_file"

This generated a new narrowPeak file, which I then used to produce the GFF file. However, this process resulted in the hockey stick plot not being smooth.

Now, if I open the .narrowPeak file in Excel and use its filtering function to remove these non-standard chromosome lines, the resulting hockey stick plot looks perfectly normal. Could you please explain why this happens?"