Error of Trinity Abundance estimation using RSEM

Question

[pr.khavari]

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.

[h.mon]

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

[st.ph.n]

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

Answer 1

[st.ph.n]

Change /--right to --right.