Hi,
I have an alignment of human data (a small bam file with less than 1M reads), and would like to calculate and plot the coverage around specific genomic features.
Specifically, I would like to calculate coverage of 100Kbp before and after each Transcription Start Site (TSS). This can be made in windows of 1000bp. I tried different methods, mostly with R and GRanges, but couldn't get the results because of the dimension of the outputted files. The probelm is that all TSS are around 200'000, so you can imagine how gigantic the outputs are.
An average of of the values for each window will also work (i.e. for each 1Kbp window between +100Kbp and -100Kbp around each TSS, I can plot the average of all windows with the same distance from each TSS).
Are there any program or memory-saving methods to do this?
Thanks in advance.
I have an alignment of human data (a small bam file with less than 1M reads), and would like to calculate and plot the coverage around specific genomic features.
Specifically, I would like to calculate coverage of 100Kbp before and after each Transcription Start Site (TSS). This can be made in windows of 1000bp. I tried different methods, mostly with R and GRanges, but couldn't get the results because of the dimension of the outputted files. The probelm is that all TSS are around 200'000, so you can imagine how gigantic the outputs are.
An average of of the values for each window will also work (i.e. for each 1Kbp window between +100Kbp and -100Kbp around each TSS, I can plot the average of all windows with the same distance from each TSS).
Are there any program or memory-saving methods to do this?
Thanks in advance.
Comment