Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
Entering edit mode
Leon • 0
Last seen 13 days ago
United States


I noticed a previous post:

I think what we can do is to add another parameter to featureCounts
to let the function reduce the read to its 5' most base or its 3' most
base, before carrying out read counting. With this parameter, you can
get the start or end position of a read and then use 'readExtension5'
and 'readExtension3' to extend the read to an arbitrary length (the
readExtension options will be applied to the single base position the
read is reduced to)

According to the description above, the order of read manipulation should be shift > reduction > extension. However, the implementation is shift > extension > reduction, as described in the User Guide. As a consequence, users can not extend reads to a fixed length (e.g., 150) from their 5' end. Therefore, I request one option to enable the switch of the order of read manipulation between shift > reduction > extension and shift > extension > reduction, or one option (namely readExtensionFrom5) that reads can be extended from their 5' end. The requested option can make featureCounts manipulate reads more flexible, especially in the case that reads need to shift first and then be extended to a fixed length for peak calling. An example is to count reads in ATAC-seq peaks and then perform further downstream analysis. In the step of ATAC-seq peak calling (using --shift and --extsize in MACS2), reads are usually shifted -75 nt and then extended to 150 nt from their 5' end.

SubRead featureCounts • 52 views

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