Question: Fastq Groomer Before Bwa Mapping ?
gravatar for Praveen Raj Somarajan
7.0 years ago by
Praveen Raj Somarajan100 wrote:
All, I'm wondering why do we need to convert Illumina FASTQ into sanger using FastQ Groomer before mapping with BWA in galaxy. The lastest version of BWA itself added -I option to use Illumina data directly. What's your opinion on this? Secondly, I found that "Map with BWA for Illumina" uses -I option in the commandline during execution, even for sanger formatted reads. How does it impact the results? Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD
bwa alignment • 1.0k views
ADD COMMENTlink modified 7.0 years ago by Peter Cock1.4k • written 7.0 years ago by Praveen Raj Somarajan100
gravatar for Peter Cock
7.0 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
As the name suggested, original that wrapper assumed Illumina FASTQ encoding. This was fixed in August 2011 using a patch from Assaf Gordon, see Issue 635. Which Galaxy instance are you using, and when was it last updated? Peter
ADD COMMENTlink written 7.0 years ago by Peter Cock1.4k
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