Use of Deconseq chromosome libraries
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6.7 years ago

Dear all,

I created a database with the human sequences using the following command:

bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1

This 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 for 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. And I fear to try all possible combinations.

What would be the correct use of Deconseq with the human library to remove the human contaminants?

Thank you

human-contaminants deconseq • 1.6k views
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