Question: "islands" and number of reads in the island in package chipseq/ShortRead
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gravatar for Nora Rieber
9.9 years ago by
Nora Rieber40
Nora Rieber40 wrote:
Dear all, I'm looking for a fast way of computing how many reads map into a certain location (e.g. between position 300 and 400 on chromosome 14). Is there any function to compute this in the packages chipseq or ShortRead? After reading the vignette for chipseq, I thought viewSums(islands) computes the number of reads, but it seems to compute the sum of the coverage. I've written my own code to do this but it is pretty slow and I wonder if there's a better way. Thanks, Nora
chipseq coverage • 436 views
ADD COMMENTlink modified 9.9 years ago by Kasper Daniel Hansen6.4k • written 9.9 years ago by Nora Rieber40
Answer: "islands" and number of reads in the island in package chipseq/ShortRead
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gravatar for Kasper Daniel Hansen
9.9 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
The best way to do this with IRanges is to make the reads into a set of IRanges with width 1, make your regions into IRanges as well and then use findOverlaps. You need to do this by the chromosome, so you might want to use stuff like IRangesList and RangedData. This is pretty fast but requires that all reads fit into memory. An alternative is to use the Genominator package that was designed for this task. That will require some overhead in learning how to use it (= reading the vignette). Kasper On Dec 1, 2009, at 7:17 AM, Nora Rieber wrote: > Dear all, > > I'm looking for a fast way of computing how many reads map into a > certain location (e.g. between position 300 and 400 on chromosome 14). > > Is there any function to compute this in the packages chipseq or > ShortRead? After reading the vignette for chipseq, I thought > viewSums(islands) computes the number of reads, but it seems to compute > the sum of the coverage. > > I've written my own code to do this but it is pretty slow and I wonder > if there's a better way. > > Thanks, > Nora > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.9 years ago by Kasper Daniel Hansen6.4k
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