Using variable read length in rmats

[Odudu James]

Performing fastqc on all my fastq files for both tumor and normal samples, i have that the read length for each fastq file is 25-50 (so its a range). My question is those this code look right?

run_rmats --s1 "~/Tumor-.txt" \
--s2 "~/Normal.txt" \
--gtf "~/hg38.ncbiRefSeq.gtf" \
--bi "~/indexUCSC_GENCODE" \
-t paired \
--readLength 50 \
--variable-read-length \
--nthread 8 \
--od "~/rmats_output" \
--tmp "~/rmats_temp"

I am making the choice to use the readLength as 50 since its the maximum length in the dataset. 

[Changhe Ji]

Tumor-.txt changes to s2.txt Normal.txt changes to s1.txt and follow the instructions of https://github.com/Xinglab/rmats-turbo

Odudu James <odudua...@gmail.com> 于 2025年4月28日周一 13:31写道：

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