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Old 06-28-2012, 09:31 AM   #1
ParthavJailwala
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Location: Maryland, USA

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Default SICER: redundancy threshold parameter

I am looking for some help in setting the 'redundancy threshold' parameter that is to be specified while running SICER for calling peaks from histone data. The protein of interest here is a high mobility group nucleosome binding protein (HMGN1) which is predicted to have broad histone-like peaks.

As I do not want to remove duplicate reads from the input BED file, what do I specify for the 'redundancy threshold' on the command line. I am not able to leave it blank, as SICER expects something in that field.

I will appreciate any help or pointer in setting this parameter.

Thanks
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Old 08-07-2012, 02:55 AM   #2
Kulvait
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Default

The redundancy threshold parameter is handled by python script src/remove_redundant_reads.py

Code:
if current_count <= cutoff:
     o.write('\t'.join(sline)+'\n')
     retained += 1
If you really want to retain all the duplicates in your bed file then you have to set this parameter (cutoff) higher than maximum number of duplicates in your bed file. 2147483647 should be in most cases OK

Duplicate is defined like a reed with the same start and stop coordinate, some orientation on the same chromosome. If there will be for example 2147483645 reads of the same specification above it will be then retained.
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