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dead link featurecounts
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Geert van Geest committed Nov 5, 2021
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Expand Up @@ -85,7 +85,7 @@ gunzip Araport11_GTF_genes_transposons.Mar202021.noChr.gtf.gz
* What are the alignment rates?
* How do the aligners handle splicing?
* How are spliced alignments stored in the SAM file? (have a look at the CIGAR string)
* What would be the effect of the aligner if you would be measuring gene expression? (To investigate this you'll need to run [featureCounts](http://bioinf.wehi.edu.au/featureCounts/)).
* What would be the effect of the aligner if you would be measuring gene expression? (To investigate this you'll need to run [featureCounts](http://subread.sourceforge.net/featureCounts.html)).
* What is the effect of setting the option `-Q` in `featureCounts` on the comparison between the aligners?

!!! hint "Run your processes on multiple cores!"
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* What are the alignment rates?
* How do the aligners handle splicing?
* How are spliced alignments stored in the SAM file?
* What would be the effect of the aligner if you would be measuring gene expression? (To investigate this you'll need to run [featureCounts](http://bioinf.wehi.edu.au/featureCounts/)).
* What would be the effect of the aligner if you would be measuring gene expression? (To investigate this you'll need to run [featureCounts](http://subread.sourceforge.net/featureCounts.html)).
* What is the effect of setting the option `-Q` in `featureCounts` on the comparison between the aligners?

!!! hint "Run your processes on multiple cores!"
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