Question: GenomicRanges::summarizeOverlaps without strands?
0
gravatar for Sang Chul Choi
7.7 years ago by
Sang Chul Choi230 wrote:
Hi, Can I use GenomicRanges::summarizeOverlaps without strand information? I have short reads without strand information, and I want to count them on GRanges object. Can I simply set strand "*" for both GRanges object and GappedAlignments object? If that is the case, can I use readBamGappedAlignments to set strand "*"? Thank you, SangChul
• 611 views
ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Sang Chul Choi230
Answer: GenomicRanges::summarizeOverlaps without strands?
0
gravatar for Sang Chul Choi
7.7 years ago by
Sang Chul Choi230 wrote:
I might answer to my question. Maybe I could just set "+" to all of the features not "*". I think strand(GappedAlignments object) <- '+' would set '+' to all of the reads. But, I will appreciate if someone answer whether this approach would do what I want. Thank you, SangChul On Apr 5, 2012, at 5:03 PM, Sang Chul Choi wrote: > Hi, > > Can I use GenomicRanges::summarizeOverlaps without strand information? I have short reads without strand information, and I want to count them on GRanges object. Can I simply set strand "*" for both GRanges object and GappedAlignments object? If that is the case, can I use readBamGappedAlignments to set strand "*"? > > Thank you, > > SangChul > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.7 years ago by Sang Chul Choi230
Hi, Yes, you can use summarizeOverlaps() without strand information. You can reset the strand to "*" for the 'query' or just set ignore.strand = TRUE when calling summarizeOverlaps(). For details of how to set the strand see ?strand. If your bam file does not have strand information readBamGappedAlignments() should read the data into a GappedAlignments class with strand "*". Valerie On 04/05/2012 02:24 PM, Sang Chul Choi wrote: > I might answer to my question. Maybe I could just set "+" to all of the features not "*". I think strand(GappedAlignments object)<- '+' would set '+' to all of the reads. But, I will appreciate if someone answer whether this approach would do what I want. > > Thank you, > > SangChul > > On Apr 5, 2012, at 5:03 PM, Sang Chul Choi wrote: > >> Hi, >> >> Can I use GenomicRanges::summarizeOverlaps without strand information? I have short reads without strand information, and I want to count them on GRanges object. Can I simply set strand "*" for both GRanges object and GappedAlignments object? If that is the case, can I use readBamGappedAlignments to set strand "*"? >> >> Thank you, >> >> SangChul >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.7 years ago by Valerie Obenchain6.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 322 users visited in the last hour