Question: Error of Trinity Abundance estimation using RSEM
0
gravatar for pr.khavari
18 months ago by
pr.khavari0
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:

./align_and_estimate_abundance.pl --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/align_and_estimate_abundance.pl --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 :

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/align_and_estimate_abundance.pl line 283.

Thanks a lot for any valuable suggestion.

ADD COMMENTlink modified 18 months ago by st.ph.n2.4k • written 18 months ago by pr.khavari0

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

ADD REPLYlink written 18 months ago by h.mon24k

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 18 months ago by st.ph.n2.4k
3
gravatar for st.ph.n
18 months ago by
st.ph.n2.4k
Philadelphia, PA
st.ph.n2.4k wrote:

Change /--right to --right.

ADD COMMENTlink written 18 months ago by st.ph.n2.4k
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