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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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Multiple BAM input #19

Closed hatran22 closed 1 year ago

hatran22 commented 2 years ago

Would it be possible to input multiple BAMs at the same time? It seems that building the Gene index takes quite a long time and the is redundant if one is to process multiple BAMs file.

olivertam commented 2 years ago

Hi,

Thank you for your interest in the software. TElocal is designed to run on one BAM at a time, since it enables parallelization with many BAM files. I agree that building the gene index might take a long time, and it is possible to pre-built the gene index if you're using the same one frequently. You can try using TElocal_indexer to prebuilt the gene index:

usage: TElocal_indexer [-h] --afile annotation-file --itype index-type
                       [--verbose verbose] [--version]

Building an index for the genome or transposable element annotations file.

optional arguments:
  -h, --help            show this help message and exit
  --afile annotation-file
                        file for indexing of annotations
  --itype index-type    index type to build for this gtf (gene or TE)
  --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_indexer --afile gene_annotation.gtf --itype gene

The example usage should allow you to prebuilt the index, which you can then use as the gene GTF in your TElocal run. Please let us know if you encounter any issues.

Thanks.