Assembly Of Paired And Unpaired Sequences

Question: Assembly Of Paired And Unpaired Sequences

5.0 years ago by

Prash • 20

Denmark

Prash • 20 wrote:

Dear All Greetings! I am analysing a genome of ca. 3.4Mb where I have paired.fa and unpaired.fa files as of now. The sequences have been trimmed before that. Now when I assemble these reads using 'ssake -f paired -g unpaired ...', it takes hell lot of time. Perhaps, I am running out of memory in analyzing the sequence reads. I could use galaxy platform, but would like to stick with ssake. Few questions: What if I concatenate these two files, would I be able to peruse this for blasting against my reference? At this point, how do I know whether or not paired or single-end reads are better? How do I know the two chromosomal sequences? Help appreciated for stupid questions :) Thank you in advance Prash Prashanth Suravajhala, PhD. Homepage: http://www.bioinformatics.org/wiki/Prash Linkedin: http://dk.linkedin.com/in/prashbio <http: dk.linkedin.com="" in="" prashbio=""> What counts in life is not the mere fact that we have lived. It is what difference we have made to the lives of others that will determine the significance of the life we lead. Nelson Mandela

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modified 5.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.0 years ago by Prash • 20

5.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Prash, You have reach the galaxy-user@bx.psu.edu mailing list that supports the public Galaxy instance at http://usegalaxy.org. Sometimes we can help with broader questions, but for general bioinformatics help I would search, then ask, the communities at a web sites such as biostars.org and seqanswers.com. The original tool author and any web sites they support are also good resources. That said, to give some short help for your questions (but follow up with the above): 1 - most any short read dataset can be run with blast - so I am not sure what you are asking. when you ask at the other sites, add more details about your goal. 2 - running a tool such as FastQC can give you an idea about sequence quality (if that is what you mean by "better"). some tools require paired end data, so that could make it automatically better. If you are wondering which set is contributing in a "better" way to the assembly, then asking other users of the tool, ideally working with a similar genome, how they determine this would be a good place to start. 3 - to annotate assembly results with chromosome assignment - how to do this depends on what other data is available for your genome (genomic or transcripts/genes). Or what related genomes may be available (comparative). The basic idea would be to compare against known to make assignments. There is a repository for this tool in the Galaxy Tool Shed, for use to local or cloud instances, but it sounds like you already saw that. http://usegalaxy.org/toolshed. If you had technical problems with that tool, the tool author could be contacted. Although if the tool fails on the line command, then there is likely a bigger issue as you suspect (memory or otherwise), and the wrapper would be unlikely to change that. But, you could also move to a cloud instance with more resource. http://usegalaxy.org/cloud Good luck! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you Jennifer. That was a big help :) Regards Prash Prashanth Suravajhala, PhD. Homepage: http://www.bioinformatics.org/wiki/Prash Linkedin: http://dk.linkedin.com/in/prashbio <http: dk.linkedin.com="" in="" prashbio=""> What counts in life is not the mere fact that we have lived. It is what difference we have made to the lives of others that will determine the significance of the life we lead. Nelson Mandela

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