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RitchieLabIGH / IRFinder

MIT License
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I want to use Nanopore_cDNA_data #34

Open tabatakenshiro opened 1 year ago

tabatakenshiro commented 1 year ago

Thank you for creating such a useful tool! I am interested in analyzing RNA-seq data, sequenced with Nanopore's PromethION, using IRFinder-S. The raw fastq formatted data from Nanopore are stored as around 19,000 individual fastq files in a directory named "fastq_pass". After reviewing your GitHub page, I considered using the following command for analysis with IRFinder-S:

sh

bin/IRFinder Long -r REF/Human-hg19-release75 -d Output_Directory_Name input.fastq

However, I am wondering if it is possible to specify a directory for the input.fastq part, given that the single-end data from Nanopore are split into around 19,000 files.

I look forward to your guidance on this.

Thank you very much. Best, Kenshiro

CloXD commented 1 year ago

Dear Kenshiro, First of all, thanks for using IRFinder-S. You need to merge the fastq files in a single entry ( https://denbi-nanopore-training-course.readthedocs.io/en/latest/basecalling/merge.html ) Cheers, Claudio

tabatakenshiro commented 1 year ago

Thank you very much. I followed the instructions provided in the URL and successfully merged the files into a single one. The file format is fastq.gz; is that okay?