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Ribosome profiling data analysis PEAK FINDER ALGORITHM
Hi all,
I am working on ribosome profiling seq-data, obtained after blocking translation using Harringtonine.
It's single-read, 50 cycles sequencing, from Illumina.
I was looking at algorithms that can be used to call peaks (in this case to call translation start sites).
All the peak-finder algorithms I ve found so far (such as MACS, or QuEST) are used normally in ChipSeq data, but the problem is that those are based on the so called "bimodal enrichment pattern".
RPF (ribosome protected fragments) reads do not show the same bimodal pattern, therefore I cannot use those.
Does anyone have any idea of what kind of algorithm to use of the available ones?
Thanks a lot!
EdK
I am working on ribosome profiling seq-data, obtained after blocking translation using Harringtonine.
It's single-read, 50 cycles sequencing, from Illumina.
I was looking at algorithms that can be used to call peaks (in this case to call translation start sites).
All the peak-finder algorithms I ve found so far (such as MACS, or QuEST) are used normally in ChipSeq data, but the problem is that those are based on the so called "bimodal enrichment pattern".
RPF (ribosome protected fragments) reads do not show the same bimodal pattern, therefore I cannot use those.
Does anyone have any idea of what kind of algorithm to use of the available ones?
Thanks a lot!
EdK
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