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speciationgenomics / data

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Seek for the missing data file"genome_scan/chrEnds.txt" #2

Open ShirelyI opened 2 years ago

ShirelyI commented 2 years ago

Hello Joana / Mark I came across your excellent tutorial on analyzing speciationgenomics . I am recently practising with a dataset you used in the course ,there seems to be some missing data files. For example, I could not find "./genome_scan/chrEnds.txt" in the data section. Could you please help with this file? thanks ShirelyI

rturba commented 2 years ago

Yeah, I would like to also see what that looks like. I just made assumptions of what it would be, but I'm getting some weird results, so it would be great to see if the issue is the file or the code. Thanks so much for this tutorial. It's been saving my life <3

atengstedt commented 2 years ago

Hi! Stumbled upon this issue while I was searching for answers for another problem. The file chrEnds.txt is just a simple file containing two tab delimited columns with a header, like below. The first column contains chromosome/scaffold names as in the data. The second column is the length of each chromosome + however much space you want between each chromosome in the manhattan plot. In the below example I'm analyzing European eel. First chromosome is 88.06 Mb long, and I've added 5 Mb, to get a sufficient amount of white space before the next chromosome is plotted next to it.

chr end Chr_01 93060000 Chr_02 81640000 Chr_03 76680000 Chr_04 73140000 Chr_05 71100000 Chr_06 67030000 Chr_07 62210000