Originally posted by dpryan
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Next: Having recently finished my Bioinformatics PhD in statistical methodology and vaccine development, the world of NGS is new to me!

Finally: I am using the STAR aligner (STAR_2.4.0h1) and I have build genome indices using GRCh38 [1] as described in [2]. I have then aligned my human 101bp Illumina paired-end reads to this build, using options "ENCODE standard options for long RNA-seq" in [2] section 3.2.1 and then finally I am trying to use featureCounts (Version 1.4.6) to generate a count matrix. Based on this I aim at performing DEG analysis.
Questions:
a) Is this approach valid/recommendable or have I missed something?
b) Given the above scenario, would you recommend using the 'primary' or the 'top level' assembly?
c) Any other input?
Cheers again!
1. ftp://ftp.ensembl.org/pub/release-78...assembly.fa.gz
2. https://github.com/alexdobin/STAR/bl...STARmanual.pdf
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