Hello Everyone,
I have done multiplex PCR of 13 human genes and then sequenced them. My research question was to find out the even amplification of all the fragments by multiplex PCR.
The sequencing data was cleaned, aligned with the human reference genome. I have the sorted BAM file. How may I know the depth of each fragment that is aligned? How may I answer my research question from this ?
Thank you for your help. I can provide my workflow if anyone needed.
Thank you. I have tried mosdepth using the sorted bam file. The output is like this-
How may I understand the read number or depth from this?
Thank you for your help. Please let me know if I miss something.
You can provide a BED file here but looks like you already have the result from
pandepth
below. Herechr3
shows a mean coverage of (12924). This is slightly different frompandepth
result (12098) but similar. Probably because of differences in how reads are calculated in two programs.I have also used pandepth. But I could not understand the results. How can I calculate the read number? I have attached a picture of the output. I have used both bam and bed file in this case.![enter image description here](/media/images/5b004be0-207a-46c7-9a92-abb20aee)
Header row is self explanatory. It tells you how many reads there are covering the region (TotalDepth) and the mean depth in last column.