Question: Trinity Error with the the flag of --run_as_paired
0
gravatar for seta
4.1 years ago by
seta1.2k
Sweden
seta1.2k wrote:

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?

sequencing rna-seq assembly • 1.5k views
ADD COMMENTlink modified 4.1 years ago by Devon Ryan91k • written 4.1 years ago by seta1.2k
1
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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 --.
 

ADD COMMENTlink written 4.1 years ago by Devon Ryan91k

Thanks so much. 

ADD REPLYlink written 4.1 years ago by seta1.2k
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