Few general queries

[ashokpatowary]

Hi @TBradley27

This tools really great. I am having few very basic question. Can you please provide your input on it.

1. Can I provide an independent gtf file (non-gencode) as transcript input?
2. Can the specify the parameters for transcript expression?
3. Finally, have you tried it on long read fastq files?

Thanks

[TBradley27]

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:

1. 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 (Enable processing of non-Ensembl GTF files #8) specifically for this point.

2. 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 Move rule configuration values backwards into YAML config files #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.

3. 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