Program options for trinity_gene_trans_map: 

Can't open --help: No such file or directory at /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/get_Trinity_gene_to_trans_map.pl line 7.


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Program options for samtools_faidx: 

Usage: samtools faidx <file.fa|file.fa.gz> [<reg> [...]]
Option: 
 -o, --output FILE        Write FASTA to file.
 -n, --length INT         Length of FASTA sequence line. [60]
 -c, --continue           Continue after trying to retrieve missing region.
 -r, --region-file FILE   File of regions.  Format is chr:from-to. One per line.
 -i, --reverse-complement Reverse complement sequences.
     --mark-strand TYPE   Add strand indicator to sequence name
                          TYPE = rc   for /rc on negative strand (default)
                                 no   for no strand indicator
                                 sign for (+) / (-)
                                 custom,<pos>,<neg> for custom indicator
 -f, --fastq              File and index in FASTQ format.
 -h, --help               This message.


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Program options for trinity_fasta_seq_length: 

Error: Couldn't open --help


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Program options for trinity_stats: 

Error: Couldn't open --help


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