Trinity Question

Question

[jasonwufree2012]

Hi， I 'd like to use Trinity to analyze my strand-specific pair-end sequencing data (dUTP) and I am very confused about how to choose the argument. I got two reads files, _1.fa and _2.fa. For --SS_lib_type argument ,I choose RF.As described in tophat manual for dUTP(graph below), reads from _1.fa are from the right-most end of the fragment(in transcript coordinates), and _2.fa are from the left-most . So ,when I run trinity ,should I choose _1.fa for argument --right, and _2.fa for --left.In the command line "Trinity.pl --seqType fa --left left.fa --right right.fa --CPU 4 --JM 4G", dose the left.fa always means _1.fa?

Answer 1

[rtliu]

As far as I understand, -left parameter always indicates _1.fa or _1.fq; -right parameter always indicates -2.fa or _2.fq. -left and -right parameters have nothing to do with the actual read location in the final transcripts, therefore your command may look like:

Trinity.pl --seqType fa --left reads_1.fa --right reads_2.fa --SS_lib_type RF --CPU 4 --JM 100G

More details can be found on Trinity screencast.

[jasonwufree2012]

Thanks for your answer!