I was having the same question as the original poster, and although this is an old question, I wanted to post an answer:
MAGeCK
now has paired-end read support:
https://bitbucket.org/liulab/mageck/commits/3e3344e64f0dc2d5b20f5895a9c995b5a9cd0124
You use the --fastq-2
option, as follows:
mageck count -l library.txt -n prefix --sample-label A,B,C,D --fastq A_1.fq.gz B_1.fq.gz C_1.fq.gz D_1.fq.gz --fastq-2 A_2.fq.gz B_2.fq.gz C_2.fq.gz D_2.fq.gz
In the example above, we have four samples: A, B, C, D, each of which are associated with a pair of fastq files (for paired-end reads). For example, sample A has A_1.fq.gz and A_2.fq.gz associated with it. The order of the files in the --fastq-2
option should be consistent with the order in the --fastq
option. The way the algorithm works (or at least my understanding of it): iff the first read pair doesn't map successfully, then it will try mapping the second read pair.
(Note: The above applies to the current MAGeCK
version: 0.5.9.2
).
Hi there, I'm not a MAGeCK expert, but I find it difficult to understand what you're trying to achieve. I encourage you to improve your title (e.g. include MAGeCK and PE) to help the right people find your post