I'm trying to use bamCoverage to convert my TopHat bam files into bigwig files for visualization on UCSC genome browser. bamCoverage asks for the Effective Genome Size and if I'm using the zebra fish DanRer10 genome, does anyone know what the effective genome size would be for that?
Also, this is the information it gives about what the effective genome size is: "The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."
I cam across the number 1371719383, but I think that is the total length rather than just the mappable length?
Thanks for any help!