mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
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The -trim option #34

Closed StevenWingett closed 2 years ago

StevenWingett commented 2 years ago

Hi,

Firstly, thank you for making this great tool available to the bioinformatics community. I have a question about the -trim option. It is mentioned in the README.md file:

-trim : allow trimming (default: false)

But this option is not present in the run_rcorrector.pl help message, nor is this option allowed by the this script.

I presume that the run_rcorrector.pl script has changed but the README.md has not been updated accordingly. I was just wondering, does this mean that the tool will accept quality-trimmed FASTQ files by default?

Many thanks for your assistance.

Regards, Steven

mourisl commented 2 years ago

Thanks for finding this error! The trim feature is removed because it may remove valuable information for lowly expressed transcripts. I have updated the README flie.

Rcorrector can take fastqs with varied read length, so you can directly use quality-trimmed FASTQ file as input.

StevenWingett commented 2 years ago

Great, thanks for letting me know.

Steven