Comments (1)
Hi @ashokpatowary,
Thank you very much for getting in touch about these issues. I am glad the tool is of interest to you.
I will try and address your message point-by-point:
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This is a good point you make, and this is a known limitation of FilTar. Currently FilTar only accepts Ensembl/Gencode formatted GTF files. This is an active area of development, and I look forward to updating you once this issue has been addressed. I have created a new issue (#8) specifically for this point.
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More accessible and extensive configuration options is also something that I am currently looking into. This is an issue that has partially been raised previously ( see #5). However, I now also see the need to include more comprehensive configuration options. Can you tell me please which transcript expression parameters you are most interested in please? As a short-term workaround, you could try editing the file 'FilTar/modules/quant_reads/salmon/quant_salmon.py' in order to specify parameter values directly in this wrapper script. However, I am hoping to implement a more user-friendly method of specifying these configuration options.
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At the moment, FilTar has only been tested with Illumina short-read data. However, integrating long-read data would be an exciting opportunity for the future. Could you specify which type of long-read data you are interested in please i.e. which sequencing technology/platform?
If you have any more comments or queries about the tool then do not hesitate to get in contact.
Many thanks,
Thomas
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Related Issues (20)
- Reduce inefficiency in use of whole-genome alignments
- Improve cluster support/integration
- Manage targetscan dependencies within a single conda environment
- Version tracking of dependencies
- Make use of snakemake resource usage profiles
- Linting and formatting
- Allow the user to set library type if this information is known in advance
- Switch away from using three letter species initials
- Process genomic data not split into sequencing block (i.e. contig level assemblies)
- Switch to using toplevel genomes only
- Add a line at the top of each script stating its function
- Implement a more sophisticated method of mapping chromosome/scaffold identifiers
- Generate a report regarding the extent of 3'UTR reannotation
- Add rule to validate generated bedgraph files
- Speed up the process of generating average bedgraph coverage values from many bedgraph files
- Add gene symbol metadata when executing APAtrap
- Standardise and minimise name space throughout the repository
- Eliminate use of shell scripts
- Where appropriate denote rule input/output dependency relationships explicitly
- FilTar error message HOT 1
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