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7.0 years ago
pr.khavari
•
0
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.
Please use the
code
button to format code, commands and such.Why do you
cd
to this directory:cd /media/marziyeh/56F72A78084DABD5/RNA-seqdata/
, the specify the Trinity.fasta twice?