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FastUniq on linux terminal

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
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updated by Biostar Biostar • written by marongiu.luigi marongiu.luigi

What is the error you are getting?

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written by venu venu

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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written by Michael Dondrup Michael Dondrup

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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written by luigi.marongiu • luigi.marongiu

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

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written by h.mon h.mon

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

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written by luigi.marongiu • luigi.marongiu

1 answer

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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written by h.mon h.mon

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