FastUniq on linux terminal
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6.9 years ago

Dear all,

I am trying to use fastUniq to remove duplicated sequences. I am using the following command on linux platform:

~/FastUniq/source/fastuniq -i <seq1.fq> <seq2.fq> -tq -o fu_1.fq -p fu_2.fq  -c 0

But I got an error. I tried also different versions of –t but did not work…

I found the manual a bit spartan, could you please give some tips on how to write the command?

Thank you

next-gen • 5.2k views
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Questions only stating "I got an error" but give no further details about the nature of the error or specific messages, should be closed as "Not specific enough to answer" in the future, to discourage this.

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I am getting: $ Error in open left fastq file @M03595:11:000000000-AG58B:1:1101:16029:1738 1:N:0:26 for read!

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If you carefully read my answer bellow, you will find out what went wrong.

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Thanks, it worked by providing the list of <seq1.fq> <seq2.fq>

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What is the error you are getting?

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6.9 years ago
h.mon 34k

FastUniq accepts as input a file listing the fastq file names.

$ ~/FastUniq/source/fastuniq -i list.txt ...

list.txt:

$ cat list

seq1.fq

seq2.fq

See here for a trick to using compressed fastq files.

edit: as venu commented, it is always helpful to copy here the exact error message, instead of just saying "it did not work".

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