How to splice the genome into many 700bp fragments ramdonly

Question

[jinxyhucy521]

To test the performance of my model ,I have splice the genome into many 700bp fragments randomly,which

could be used to construct the negtive and positive examples.I have used the R splice the genome

into many 700bp fragments orderly rather than randomly!!!

Answer 1

[microfuge]

Check out bedtools random command http://bedtools.readthedocs.io/en/latest/content/tools/random.html

[jinxyhucy521]

Thanks for your reply very much!!This is a very useful tool!!!

Answer 2

[Brian Bushnell]

Using the BBMap package:

randomreads.sh in=genome.fasta out=fragments.fasta length=700 reads=1000000 adderrors=f

That will give randomly-distributed sequences... alternatively:

shred.sh in=genome.fasta out=fragments.fasta length=700

That will produce evenly-spaced sequences; you can adjust the spacing with the "overlap" flag.

[jinxyhucy521]

2_chr1_1_1481410_1482109_1473410_NC_000853.1 Thermotoga maritima MSB8 chromosome, complete genome Dear Brian Bushnell,I have used your tools,and the result is the upper,I set the length=700,I have read your readme file,but I can't find the meaning of chr1_1_1481410_1482109_1473410...Could you tell me this meaning?

[Brian Bushnell]

"1473410" is the start position, and the part after (NC_000853.1 Thermotoga maritima MSB8 chromosome, complete genome) is the name of the sequence it came from. The parts before that are internal BBMap coordinates and not very useful. So, that sequence was 700 bp from "NC_000853.1 Thermotoga maritima MSB8 chromosome, complete genome" starting at position 1473410 (zero-based). Meaning, the first base in the sequence would be numbered 0.

[jinxyhucy521]

I think if the 1473410 is the starting,which one is the ending?And I have another question:does the

result has the fragments from complementary strand?