Reads were trimmed using cutadapt (40) and mapped to the human genome GRCh38 using STAR (41) v2.4.2a (with End To End option and out Filter Mismatch NoverLmax set to 0.04). Counting proceeded over genes annotated in Ensembl release 88, using an HTSeq count (42) (intersection-strict mode). Differential expression analysis was performed using DESeq2 (43) with the betaPrior, cooksCutoff, and independent Filtering parameters set to false. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg (44). The pipeline was constructed using Snakemake (45).

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.