From 6e018e1542e038fe0150418214bf2d9869c68beb Mon Sep 17 00:00:00 2001 From: "Michael A. Boemo" Date: Mon, 4 Mar 2019 09:50:54 +0000 Subject: [PATCH] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f75e330..fa801ae 100755 --- a/README.md +++ b/README.md @@ -40,9 +40,9 @@ which will put a file `output.psl` in your working directory. If you can approximate the probability at which cannonical bases are substituted for an analogue in an analogue-rich region, DNAscent can use the output from `DNAscent detect` to call regions of analogue incorporation. Run, ```shell -bin/DNAscent regions -d output.detect -p 0.2 -o output.regions +bin/DNAscent regions -d output.detect -o output.regions ``` -where `p` is the probability that there is an analogue in any 6mer. The file `output.regions` will have the same header for each read as in `output.detect`. The first column specifies where the region started, the second column specifies where the region ended, and the third column gives a z-score specifying how well this region fit the model for analogue incorporation. Scores near or above 0 indicate that this region fit the model well and is most likely a region of analogue incorporation. Negative scores indicate that there were fewer analogue calls than would be expected in an analogue region. The DNAscent regions executable can also call fork direction and origin location. To enable this functionality, add the `--replication` flag when you call DNAscent regions. This will produce a file `calledOrigins.dnascent` that lists the chromosomal coordinates of called origins on individual reads. +The file `output.regions` will have the same header for each read as in `output.detect`. The first column specifies where the region started, the second column specifies where the region ended, and the third column gives a z-score specifying how well this region fit the model for analogue incorporation. Scores near or above 0 indicate that this region fit the model well and is most likely a region of analogue incorporation. Negative scores indicate that there were fewer analogue calls than would be expected in an analogue region. The DNAscent regions executable can also call fork direction and origin location. To enable this functionality, add the `--replication` flag when you call DNAscent regions. This will produce a file `calledOrigins.dnascent` that lists the chromosomal coordinates of called origins on individual reads. ## Runtime The runtime of DNAscent is linear with respect to the amount of data (in bases) passed to it.