TElocal: a tool that utilizes both uniquely and ambiguously mapped reads to quantify transposable element expression at the locus level.

• TElocal Github page

• Module Name: TElocal (see the modules page for more information)
• Unusual environment variables set
  • TElocal_HOME  installation directory

[user@biowulf]$ sinteractive  
[user@cn0861 ~]$ module load TElocal 
[+] Loading singularity  3.8.5-1  on cn4177
[+] Loading TElocal 1.1.2  ...

[user@cn0861 ~]$ TElocal -h 
usage: TElocal [-h] -b RNAseq.bam --GTF genic-GTF-file --TE TE-annot-file [--stranded option] [--mode TE counting mode]
               [--project name] [--sortByPos] [-i iteration] [--maxL maxL] [--minL minL] [-L fragLength]
               [--verbose [verbose]] [--version]

Measuring TE expression per-locus, per-sample.

optional arguments:
  -h, --help            show this help message and exit
  -b RNAseq.bam, --BAM RNAseq.bam
                        An RNAseq BAM file.
  --GTF genic-GTF-file  GTF or db file for gene annotations
  --TE TE-annot-file    locInd file for transposable element annotations
  --stranded option     Is this a stranded library? (forward, no, or reverse). For "first-strand" cDNA libraries (e.g.
                        TruSeq), choose reverse. For "second-strand" cDNA libraries (e.g. QIAseq stranded), choose
                        forward. DEFAULT: no.
  --mode TE counting mode
                        How to count TE: uniq (unique mappers only), or multi (distribute among all alignments).
                        DEFAULT: multi
  --project name        Name of this project. DEFAULT: TElocal_out
  --sortByPos           Alignment file is sorted by chromosome position.
  -i iteration, --iteration iteration
                        number of iteration to run the optimization. DEFAULT: 100
  --maxL maxL           maximum fragment length. DEFAULT:500
  --minL minL           minimum fragment length. DEFAULT:0
  -L fragLength, --fragmentLength fragLength
                        average fragment length for single end reads. For paired-end, estimated from the input alignment
                        file. DEFAULT: for paired-end, estimate from the input alignment file; for single-end, ignored
                        by default.
  --verbose [verbose]   Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show
                        process information, 3: show debug messages. DEFAULT:2
  --version             show program's version number and exit

Example: TElocal -b RNAseq.bam --GTF gene_annotation.gtf --TE TE_annotation.locInd --mode multi

[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226