Megahit Assembly - command line error
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2.6 years ago
yuki4208 • 0

I am new to bioinformatics and I need help:((

I have downloaded megahit and working in the 'bin' directory

  1. I dont know where I am supposed to put my samples
  2. even if I run the files with the specific directory from bin/Input/R1 and R2 nothing happens

bin$ ./megahit -1 Input/Input-1_S6_L001_R1_001.fastq.gz -2 Input/Input-1_S6_L001_R2_001.fastq.gz -o A_Input

What is wring with my command line?

assembly megahit bioinformatics fastq • 1.1k views
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Do you get an error?

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2.6 years ago
Mensur Dlakic ★ 15k

This part of your command ./megahit means that you have a megahit executable in the present directory. If that's not the case, it won't work.

This part of your command Input/Input-1_S6_L001_R1_001.fastq.gz means that in that same directory you have a sub-directory called Input, and in that sub-directory a file called Input-1_S6_L001_R1_001.fastq.gz. Same for your other paired-end file.

These are possible errors that I can point out without actually knowing the error message. It would help if you post what that error message is.

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