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 strands) --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?