I have a de novo transcriptome for a pepper plant by Trinity. After all I was trying to perform a decontamination of possible unwanted transcripts, I tried using deconseq tool but i found a problem that affects many users: does anybody knows a possible solution or another tool like deconseq? it may anything... my deconseqConfig.pm is:
use constant DBS => {hs_ref_GRCh37_1 => {name => 'Human Reference GRCh37',
db => 'hs_ref_GRCh37_1,hs_ref_GRCh37_2,hs_ref_GRCh37_3'},
bactDB_s1 => {name => 'Bacterial genomes',
db => 'bactDB_s1,bactDB_s2'},
virDB => {name => 'Viral genomes',
db => 'virDB'},
mm_red_s1 => {name => 'marmals',
db => 'mm_ref_s1,mm_ref_s2'},
archDB_s1 => {name => 'archeas',
db => 'archDB_s1'}}; use constant DB_DEFAULT => 'bactDB';
i got the following ERROR:
asus@asus-ASUS-TUF-Gaming-A15-FA506II-FA506II:~/Documentos/RNA-seq/Cc/HQ_reads/Cc_Rs/Deconseq_out$ deconseq.pl -f Trinity.fasta -DBS VirDB
ERROR: database "VirDB" does not exist in config file.
Try 'deconseq -h' for more information.
when I look for database it appears:
asus@asus-ASUS-TUF-Gaming-A15-FA506II-FA506II:~/Documentos/RNA-seq/Cc/HQ_reads/Cc_Rs/Deconseq_out$ deconseq.pl -show_dbs
archDB_s1 - archeas
bactDB_s1 - Bacterial genomes
hs_ref_GRCh37_1 - Human Reference GRCh37
mm_red_s1 - marmals
virDB - Viral genomes
or might be the kind of files of dataset? are like these:
ls dcdata1/
archDB_s1.amb bactDB_s1.amb bactDB_s2.amb bactDB_s3.amb hs_ref_GRCh37_s1.amb hs_ref_GRCh37_s2.amb hs_ref_GRCh37_s3.amb mm_ref_s1.amb mm_ref_s2.amb virDB_s1.amb
archDB_s1.ann bactDB_s1.ann bactDB_s2.ann bactDB_s3.ann hs_ref_GRCh37_s1.ann hs_ref_GRCh37_s2.ann hs_ref_GRCh37_s3.ann mm_ref_s1.ann mm_ref_s2.ann virDB_s1.ann
archDB_s1.bwt bactDB_s1.bwt bactDB_s2.bwt bactDB_s3.bwt hs_ref_GRCh37_s1.bwt hs_ref_GRCh37_s2.bwt hs_ref_GRCh37_s3.bwt mm_ref_s1.bwt mm_ref_s2.bwt virDB_s1.bwt
archDB_s1.pac bactDB_s1.pac bactDB_s2.pac bactDB_s3.pac hs_ref_GRCh37_s1.pac hs_ref_GRCh37_s2.pac hs_ref_GRCh37_s3.pac mm_ref_s1.pac mm_ref_s2.pac virDB_s1.pac
archDB_s1.rbwt bactDB_s1.rbwt bactDB_s2.rbwt bactDB_s3.rbwt hs_ref_GRCh37_s1.rbwt hs_ref_GRCh37_s2.rbwt hs_ref_GRCh37_s3.rbwt mm_ref_s1.rbwt mm_ref_s2.rbwt virDB_s1.rbwt
archDB_s1.rpac bactDB_s1.rpac bactDB_s2.rpac bactDB_s3.rpac hs_ref_GRCh37_s1.rpac hs_ref_GRCh37_s2.rpac hs_ref_GRCh37_s3.rpac mm_ref_s1.rpac mm_ref_s2.rpac virDB_s1.rpac
archDB_s1.rsa bactDB_s1.rsa bactDB_s2.rsa bactDB_s3.rsa hs_ref_GRCh37_s1.rsa hs_ref_GRCh37_s2.rsa hs_ref_GRCh37_s3.rsa mm_ref_s1.rsa mm_ref_s2.rsa virDB_s1.rsa
archDB_s1.sa bactDB_s1.sa bactDB_s2.sa bactDB_s3.sa hs_ref_GRCh37_s1.sa hs_ref_GRCh37_s2.sa hs_ref_GRCh37_s3.sa mm_ref_s1.sa mm_ref_s2.sa virDB_s1.sa
thanks for any advice or suggestion.
greetings!