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bug in the plot_homer_annotatepeaks.r script #86
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Hi @anvlasova Thanks for reporting this 👍 Would you mind uploading a file I can use to test this please? Alternatively, please feel free to submit a PR with a fix to the |
Hi @drpatelh, we found this problem with this annotation file ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.57_FB2014_03/gff/dmel-all-filtered-r5.57.gff.gz thanks, |
Thanks @anvlasova . Just to clarify this is the change you had to make in order to get things working? |
hi @drpatelh , |
I hope not! I remember specifically adding in Fixed in #92 |
Hi,
Some annotations containing special characters in the gene names, for example in dm3 genome some genes have " ' '' symbol in the gene name.
Function 'read.table' in the script plot_homer_annotatepeaks.r can't properly read such files and the whole pipeline crashes in the 'merge_library_macs_qc' step. While function read.csv can process those files without problems. Guess this is because of default quote and comment char options that are different between these two functions: https://stackoverflow.com/questions/12828438/read-csv-vs-read-table
Can you please fix it?
thanks,
Anna
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