RNA-seq: problems with DEcontamination with Deconseq
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10 days ago

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!

RNA-seq contaminants assembly De_novo • 112 views
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