These are chat archives for cboursnell/transfuse

6th
Dec 2016
Lavinia Gordon
@MrsLaviniaG_twitter
Dec 06 2016 00:44
Thanks @cboursnell for the column headers, appreciated. Ran transfuse on a single libraries with multiple assemblers - beautiful! Now I would like to combine several libraries to get a single transcriptome for a single tissue, simple approach does not work:
whoops, sorry, always forget to switch modes:

so ..

/transfuse/transfuse-0.5.0-linux-x86_64/transfuse -a transrate_R20_transfuse_cons/good.R20_transfuse_cons.fa,transrate_R35_transfuse_cons/good.R35_transfuse_cons.fa -l R20/trinity/insilico_read_normalization/left.norm.fq,R35/trinity/insilico_read_normalization/left.norm.fq -r R20/trinity/insilico_read_normalization/right.norm.fq,R35/trinity/insilico_read_normalization/right.norm.fq -o Eyestalk

/transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/lib/ruby/gems/2.2.0/gems/bundler-1.7.12/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /usr/local/appl in PATH, mode 040777
/transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:201:in populate_contig_data': undefined methodp_seq_true=' for nil:NilClass (NoMethodError)
from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:154:in block in analyse_read_mappings' from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/lib/ruby/2.2.0/csv.rb:1739:ineach'
from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/lib/ruby/2.2.0/csv.rb:1122:in block in foreach' from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/lib/ruby/2.2.0/csv.rb:1273:inopen'
from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/lib/ruby/2.2.0/csv.rb:1121:in foreach' from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:151:inanalyse_read_mappings'
from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/read_metrics.rb:73:in run' from /transfuse/transfuse-0.5.0-linux-x86_64/lib/ruby/2.2.0/gems/transrate-1.0.1/lib/transrate/transrater.rb:86:inread_metrics'
from /transfuse/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:152:in block in transrate_consensus' from /transfuse/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:148:inchdir'
from /transfuse/transfuse-0.5.0-linux-x86_64/lib/lib/transfuse/transfuse.rb:148:in transrate_consensus' from /transfuse/transfuse-0.5.0-linux-x86_64/lib/bin/transfuse:89:in<main>'

How can I pass two (or more) sets of normalized reads to transfuse? Many thanks.