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Question: remove empty short read after using trimEnds
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gravatar for Kunbin Qu
6.4 years ago by
Kunbin Qu40
Kunbin Qu40 wrote:
Hi, I have some short reads with low quality scores. I used trimEnds from the recent ShortRead package to remove those. Some reads were totally removed, but the headers were still there. Is there a simple way to totally eliminate them, not just the read contents and quality scores (now they are empty after applying trimEnds)? Thanks. -Kunbin ______________________________________________________________________ The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to postmaster@genomichealth.com and delete this message, along with any attachments, from your computer. [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.4 years ago by Martin Morgan ♦♦ 21k • written 6.4 years ago by Kunbin Qu40
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gravatar for Martin Morgan
6.4 years ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:
On 12/17/2011 09:05 PM, Kunbin Qu wrote: > Hi, > > I have some short reads with low quality scores. I used trimEnds from > the recent ShortRead package to remove those. Some reads were totally > removed, but the headers were still there. Is there a simple way to > totally eliminate them, not just the read contents and quality scores > (now they are empty after applying trimEnds)? Thanks. Hi Kunbin -- in a second pass, x[width(x) != 0]. Martin > > -Kunbin > > ______________________________________________________________________ > > The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to postmaster at genomichealth.com and delete this message, along with any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 6.4 years ago by Martin Morgan ♦♦ 21k
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