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  • Use library in Deconseq to remove human genome

    Hello,

    I am using Deconseq to remove human sequences from fastq files generated by Myseq Illumina. I created the database with the human sequences using:

    bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1
    This as created a series of files that I placed in a subfolder named refChr. The list of files is:
    hs_ref_GRCh38_p2.amb hs_ref_GRCh38_p2.pac hs_ref_GRCh38_p2.sa
    hs_ref_GRCh38_p2.ann hs_ref_GRCh38_p2.rbwt hs_ref_GRCh38_p2_split.fa
    hs_ref_GRCh38_p2.bwt hs_ref_GRCh38_p2.rpac hs_ref_GRCh38_p2_split.fa.log
    hs_ref_GRCh38_p2.fa hs_ref_GRCh38_p2.rsa hs_ref_GRCh38_p2_split_PS.fa.fasta

    I then ran the following command to use Deconseq:
    ~$ perl /usr/bin/deconseq.pl -f fu_1.fq -dbs ./refChr/hs_ref_GRCh38_p2 -i 90 -c 90 -out_dir DECONSEQ
    But I got the following error:
    ERROR: database "./refChr/hs_ref_GRCh38_p2" does not exist in config file.

    Try 'deconseq -h' for more information.
    Exit program.

    I tried with '/refChr/...' and 'refChr/...' and also with '...hs_ref_GRCh38_p2.fa' and '...hs_ref_GRCh38_p2.sa' but same error.
    Would you have some tips on how to use the library to remove the human contaminants?
    Thank you
    G

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