Question: Error of Trinity Abundance estimation using RSEM
gravatar for pr.khavari
2.7 years ago by
Iran, Tehran, University of tehran
pr.khavari0 wrote:

Hi dear friends, I have a problem with RSEM. I run my script with two ways but it gives error. my command line is here:

First command line:

./ --transcripts Trinity.fasta /media/marziyeh/56F72A78084DABD5/RNA-seqdata/Trinity.fasta --seqType fq --left /media/marziyeh/56F72A78084DABD5/RNA-seqdata/merged_32-33_trimmed.fq.gz /--right /media/marziyeh/56F72A78084DABD5/RNA-seqdata/merged_32-33_2_trimmed.fq.gz --est_method RSEM --aln_method bowtie2 --prep_reference --trinity_mode --output_dir /media/marziyeh/56F72A78084DABD5/RNA-seqdata/RESM_output/MY_RSEM_trinity_dir

second command line:

cd /media/marziyeh/56F72A78084DABD5/RNA-seqdata/;/home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/util/ --transcripts Trinity.fasta /media/marziyeh/56F72A78084DABD5/RNA-seqdata/Trinity.fasta --seqType fq --left merged_32-33_trimmed.fq.gz /--right merged_32-33_2_trimmed.fq.gz / --est_method RSEM --aln_method bowtie2 --prep_reference --trinity_mode --output_dir MY_RSEM_trinity_dir


Error, don't understand arguments: /media/marziyeh/56F72A78084DABD5/RNA-seqdata/Trinity.fasta /--right merged_32-33_2_trimmed.fq.gz / at /home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/util/ line 283.

Thanks a lot for any valuable suggestion.

ADD COMMENTlink modified 2.7 years ago by • written 2.7 years ago by pr.khavari0

Please use the code button to format code, commands and such. 101010 Button

ADD REPLYlink written 2.7 years ago by h.mon30k

Why do you cd to this directory: cd /media/marziyeh/56F72A78084DABD5/RNA-seqdata/, the specify the Trinity.fasta twice?

--transcripts Trinity.fasta /media/marziyeh/56F72A78084DABD5/RNA-seqdata/Trinity.fasta

ADD REPLYlink written 2.7 years ago by
gravatar for
2.7 years ago by
Philadelphia, PA wrote:

Change /--right to --right.

ADD COMMENTlink written 2.7 years ago by
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