Trinity Error with the the flag of --run_as_paired

Question

[seta]

I did de novo transcriptome assembly after trimming on about 320 million Illumina paired end reads (strand-specific library, FR) using CLC genomic workbench software. Now, I'm trying to perform the same assembly using Trinity (20140717) by the following code:

./Trinity --seqType fa --JM 180G --run_as_paired file1.fa --normalize_reads --SS_lib_type FR --CPU 6 --full_cleanup

But, the Trinity gives me an error, it says:

Error, do not understand options: file1.fa

and sometimes, it says:

Error, do not understand options: file1.fa and SS__lib_type FR

Actually, file1.fa is a output of CLC genomic software after trimming in FASTA format. Since I plan to compare and probably combine the assembly results derived from both, CLC and Trinity tools, I have to do trimming using CLC and then use the trimmed file as an input file for Trinity.Is there anybody with similar experience? could you please help me out to solve the problem?

Answer 1

[Devon Ryan]

For the first error, try --run_as_paired --single file.fa. The second error likely only happens if you add an extra space somewhere or leave off the --.

[seta]

Thanks so much.