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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Running with multiple inputs #56

Open amwa opened 3 years ago

amwa commented 3 years ago

Hi, What is the default method SQuIRE uses when multiple inputs are passed to "squire map"? I recently tried passing in three FASTQs and assumed the program would produce three BAM files corresponding to each of the inputs, but instead only one output BAM was produced (with the name I specified using the --name flag). Thanks so much!

rpg18 commented 3 years ago

Hi! Have you checked the loop_map.sh script? In there, you'll see an example of running squire Map for multiple inputs. Basically, it runs squire Map in a for loop. Cheers!

amwa commented 3 years ago

Thanks for pointing me to this script! So to clarify, running squire Map with multiple inputs (e.g. squire Map -1 input1_1,input2_1,input3_1 -2 input1_2,input2_2,input3_2...) does not merge the multiple inputs in any way, but instead runs squire Map on each input sequentially?

rpg18 commented 3 years ago

Actually, it should work if you separate the input files with commas. You can try and run your line of code, but without specifying sample name with --name, so it "uses basename of read1 as default" as specified in Map.py

amwa commented 3 years ago

I did separate the input files with commas when I ran it (as written above, squire Map -1 input1_1,input2_1,input3_1) but I think you are right that it may have been the "--name" flag that caused there to be only one output. I will try running it again without this flag. Thanks!!

rpg18 commented 3 years ago

Hope it works now! Cheers!

GimenaA commented 2 years ago

Hi! Have you checked the loop_map.sh script? In there, you'll see an example of running squire Map for multiple inputs. Basically, it runs squire Map in a for loop. Cheers!

@rpg18 I've tried running the loop_map.sh script, because I have multiple samples. But it gives me the following error (described here: https://github.com/wyang17/SQuIRE/issues/72#issue-1129261350). It basically concatenates the path to the files from my first sample with the path to the files from to my second sample and therefore gives me an error. Have you run loop_map.sh successfully with multiple samples? If so, how did you fix this issue?

Thank you!