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timbitz / Aligater

Software suite for detection/analysis of chimeric RNAs from LIGR-seq data
MIT License
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Error on aligater reclass (generate database) #6

Closed fgypas closed 7 years ago

fgypas commented 7 years ago

When I run the following command to generate the database: aligater reclass --uniq --save database.jlz < lig/*blast.filtered.lig I get a bash error: "ambiguous redirect."

Then I specified the files one by one like the following: aligater reclass --uniq --save database.jlz < lig/file1.blast.filtered.lig lig/file2.blast.filtered.lig

But now i get another error message: "too many arguments"

Finally I concatenated the files into one and ran aligater reclass (which worked), but I am not sure if this is a proper way of doing it. aligater reclass --uniq --save database.jlz < <(cat lig/*blast.filtered.lig)

So am I allowed to concatenate all the files and then run aligater reclass?

timbitz commented 7 years ago

For generating the database you should just combine them with cat. Then in the next step run each filtering step independently with that single database you generated.

fgypas commented 7 years ago

Great thanks a lot.