Hi, On 11/11/2012 11:23 PM, Anthony Borneman wrote: > Hi, > > I've been experimenting with Ray (hopefully the Ray Meta component but also > after digital normalization)
Ray Meta is quite good with metagenome assemblies. Our revised manuscript is now with the editor. We addressed every concern (except 1) of the reviewers. >for performing some pooled BAC sequencing experiments where the amplicons are >often present in highly >variable relative copy number. I'd like to perform some manual assessment of >the assemblies, >but it appears that the individual read names have been replaced with >numerical labels in the >AMOS file that Ray produces. Indeed, Ray does not store read names. > This makes it impossible to investigate read pair consistency in >the assembly. Not necessarily. If you have file_1.fastq and file_2.fastq (let's say with 8000000 sequences in each file), then sequence i is paired with i + 8000000 if i is in the first file. It's i - 8000000 otherwise. The same logic applies for a many-file run. > Is there a way to relate the new read names with the original ones that were > passed >to Ray, or alternatively, are the reads renamed during loading in a systematic >way so that I can >alter the resulting AMOS file before loading into hawkeye? > Yes, see above. Example: $ less SRS011098-Ray-MiniRanks-replicate-10-.2012-11-09.1/FilePartition.txt #File Name FirstSequence LastSequence NumberOfSequences 0 SRS011098/SRR062051_1.fastq.gz 0 32137140 32137141 1 SRS011098/SRR062051_2.fastq.gz 32137141 64274281 32137141 2 SRS011098/SRR062052_1.fastq.gz 64274282 96767264 32492983 3 SRS011098/SRR062052_2.fastq.gz 96767265 129260247 32492983 4 SRS011098/SRR055676.fastq.gz 129260248 129268040 7793 5 SRS011098/SRR055756.fastq.gz 129268041 129279468 11428 6 SRS011098/SRR056894.fastq.gz 129279469 129293874 14406 7 SRS011098/SRR056977.fastq.gz 129293875 129301709 7835 8 SRS011098/SRR059326.fastq.gz 129301710 166088183 36786474 9 SRS011098/SRR059327.fastq.gz 166088184 202487722 36399539 Sequences 0 to 32137140 are paired with sequences 32137141 to 64274281. > Thanks, > > Anthony > > > > Anthony Borneman > Principal Research Scientist - Molecular Biology | The Australian Wine > Research Institute > Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | > Map > PO Box 197, Glen Osmond SA 5064, Australia > T: +61 8 83136613 (direct) | F: +61 8 83136601 | > www: www.awri.com.au | AWRI Events > > This communication, including attachments, is intended only for the > addressee(s) and contains information which might be confidential and/or the > copyright of The Australian Wine Research Institute (AWRI) or a third party. > If you are not the intended recipient of this communication please > immediately delete and destroy all copies and contact the sender. If you are > the intended recipient of this communication you should not copy, disclose or > distribute any of the information contained herein without the consent of the > AWRI and the sender. Any views expressed in this communication are those of > the individual sender except where the sender specifically states them to be > the views of the AWRI. No representation is made that this communication, > including attachments, is free of viruses. Virus scanning is recommended and > is the responsibility of the recipient. > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_nov > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
