Question: IsoEM trying to run quantification but just prints out manual
gravatar for mar77
11 weeks ago by
mar7720 wrote:

I'm trying to run IsoEM2 for the quantification of my RNA-seq experiment using the command:

     isoem2 [--GTF Homo_sapiens.GRCh38.99.chr.gtf]* [--auto-fragment-distrib]* SAMPLE.sam

as per their manual, but then the output I get is just:

isoem v 2.0.0
Usage: isoem [global options]* [library options]* <aligned_reads.sam>
Or: at <aligned_reads.sam> | isoem2 [global options]* [library options]*
Mandatory global options:
-G, --GTF <GTF file>                    Known genes and isoforms in GTF format
Mandatory library options: either -a or both -m and -d must be present:
-m, --fragment-mean <Double>            Fragment length mean
-d, --fragment-std-dev <Double>         Fragment length standard deviation
-a, --auto-fragment-distrib             Automatically detect fragment length
                                          distribution from uniquely mapping
                                          paired reads (DOES NOT WORK FOR
                                          SINGLE READS)
Optional global options:
-c, --gene-clusters <Cluster file>      Override isoform to gene mapping
                                          defined in the GTF file with a
                                          mapping taken from the given file.
                                          The format of each line in the file
                                          is "isoform   gene"
-g <genome fasta file>                  Genome reference sequence (needed by
                                          some library options)
-b                                      Perform hexamer bias correction
-h, --help                              Show help
-r <Repeats GTF>                        Drop alignments falling within
                                          annotated repeats
Optional library options:
-s, --directional                       Dataset obtained by directed RNA-Seq
                                          (the strand of each read is
                                          deterministically chosen: for single
                                          reads, the read always comes from
                                          the coding strand; for paired reads,
                                          the first read always comes from the
                                          coding strand, the second from the
                                          opposite strand)
--antisense                             Directional sequencing but the reads
                                          come from the antisense
--mate-pairs                            Paired reads come from the same strand
                                          (as opposed to the default behavior
                                          where the two reads in a pair are
                                          assumed to come from opposite
--max-mismatches <Integer>              Maximum number of mismatched allowed
                                          for a read. This requires the genome
                                          sequence to be specified (see -g).
-q, --quality-scores                    Weigh the reads based on their quality
                                          scores. This requires the genome
                                          sequence to be specified (see -g).
--repeat-threshold <nbases>             Drop all reads that have more than
                                          this many bases inside annotated
                                          repeats. Default: 20.
--polyA <nbases>                        Reads have been generated from mRNAs
                                          with polyA tails of approximately
                                          the given number of bases
-o <file prefix>                        Output files prefix. It can include
                                          path. Default: same as sam file name
-O <directory prefix>                   Output directory prefix. If read
                                          alignments are read from stdin,
                                          the default value is stdinSample
-C <confidence interval (%)>            Compute expression of genes/isoforms
                                          with specified confidence intervals.
                                          Provide an integer (default: 95,
                                          bootstraps: 200)
--endseq                                Disable length normalization for data
                                          generated using 5' or 3' end-sequen-
                                          cing protocols, which generate a
                                          single fragment per cDNA molecule

It basically just prints out the manual, which does say to use isoem rather than isoem2 as the command, but when I have tried that it says

isoem: command not found

Does anyone have any idea where I might be going wrong and how to fix it?

ADD COMMENTlink modified 7 weeks ago by Biostar ♦♦ 20 • written 11 weeks ago by mar7720

Is this the literal command you are running:

     isoem2 [--GTF Homo_sapiens.GRCh38.99.chr.gtf]* [--auto-fragment-distrib]* SAMPLE.sam

Or are you running:

     isoem2 --GTF Homo_sapiens.GRCh38.99.chr.gtf --auto-fragment-distrib SAMPLE.sam
ADD REPLYlink written 11 weeks ago by h.mon31k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 867 users visited in the last hour