Epstein Barr Virus by Janos Minarovits & Hans Helmut Niller

Author:Janos Minarovits & Hans Helmut Niller
Language: eng
Format: epub
Publisher: Springer New York, New York, NY

8.This protocol assumes that quality control and filtering steps have already been performed, e.g., by the sequencing center. If not, or if this is unclear, FastQC (http://​www.​bioinformatics.​babraham.​ac.​uk/​projects/​fastqc/​) is a quick and user-friendly program to check data quality.

9.Many STAR parameters can be altered to meet the requirements of different experiments. Some common variations are listed here; many others can be found in the STAR manual at https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf.

For paired-end RNA-Seq data, simply list both read files after the --readFilesIn argument, i.e., --readFilesIn /PATH/TO/reads_1.fastq /PATH/TO/reads_2.fastq

To only report alignments for reads that map uniquely to one genomic location, add the argument --outFilterMultimapNmax 1. Or change this number to report alignments for reads that map to multiple locations in the genome. The default (as used in step 3.2) is 10: reads aligning to more than 10 genomic locations will not be reported.

Use the argument --genomeSAsparseD 2 to reduce the RAM usage. This will result in a longer run time.

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