gz process

[wyim-pgl]

Dear Sagnik Banerjee,
Finder use gunzip in RNA-Seq input, I think STAR and Olego could accept gz file, Finder might need to remove the step to facilitate the process, otherwise, it might integrate Pigz to use multithreads.
In terms of organism option, this seems for Codan, but it might need to use in STAR alignment. Since the vertebrate and in vertebrate has such a long intron, it might need to adjust the max intron option in STAR and Olego (default is 500,000) accordingly. If you use Olego as default option for plant, it might generate gene conjugation in tandem duplication. Of course, fixTranscriptsConnectingTwoTranscripts.py will resolve this.
In the part of downloading SRA, you might need to use parallelfastqdump to use multiple CPUs. Usually, bandwidth of system is limited, downloading multiple file together will not help a lot. In addition, sometimes SRA downloading is stalling and will generate error, it need to add SRA file validation step as well.
In terms of storage saving, the conversion and validation step from SRA downloading, you might need to delete them. Some part of alignment generate SAM files, you might need to add option to delete them during the process.
Thanks for this software.

[sagnikbanerjee15]

Hello @wyim-pgl,

Thank you so much for your interest in finder. I completely agree that the issue with STAR Olego and gz could be improved. I will try to address the issues and improve those.

Thank you.