Newbie dummy question, please help

[skymj]

Hi, folks:
I am doing research on Arabidopsis. The existing reference genome is on one ecotype (Col), and we have sequenced another ecotype (Ws), since we have mutants based on Ws.

What should I do if I want to use Ws as a reference genome?
I have used bowtie to align the Ws reads to Col and use Samtools/GATK try to find any indels/SNPs, however, my target is to be able to get a new reference genome based on Ws, what should I do?

Any suggestions are much appreciated.
Thx.

[mastal]

Newbie dunmmy question, please help

Hi,


You can do de-novo assembly using your Ws reads, with or without the Col genome as a reference genome.

There are many programs for de novo assembly, depending on what type of sequencing data you have, Velvet, NIRA, Soapdenovo, and many others.

best wishes,
Maria

[skymj]

Does it mean that I cannot use the already indexed reference genome at all?
Thanks for your information

Hi,


You can do de-novo assembly using your Ws reads, with or without the Col genome as a reference genome.

There are many programs for de novo assembly, depending on what type of sequencing data you have, Velvet, NIRA, Soapdenovo, and many others.

best wishes,
Maria

[jimmybee]

If you use the reference genome then the assembly will be biased. You can assembly them de novo and then compare the assembled contigs to the reference genome instead

[chadn737]

If you don't mind me asking, what exactly are you trying to do. You say you have mutants in the Ws ecotype, so are you trying to use this sequencing data to map those mutations or did you sequence WT Ws to create a reference for this purpose? Or do you need the Ws genome for other purposes? I ask, because the optimal solution for what you are trying to do may be different than what you think.

Ws is not so different from Col that it you cannot map to the Col reference.

Furthermore, the Ws genome has already been assembled as part of the 1001 Genomes project.....so, the dirty work has already been done

http://mus.well.ox.ac.uk/19genomes/fasta/

[skymj]

we have sequenced the mutants and ws. Thanks for your informaiton!!
Would you educate me with what should I do if I know the mutant has a large chunk of insertion (up to 10kb possibly) and I wish to locate it, should I use reference genome based alignment or de novo, how?
Thanks

If you don't mind me asking, what exactly are you trying to do. You say you have mutants in the Ws ecotype, so are you trying to use this sequencing data to map those mutations or did you sequence WT Ws to create a reference for this purpose? Or do you need the Ws genome for other purposes? I ask, because the optimal solution for what you are trying to do may be different than what you think.

Ws is not so different from Col that it you cannot map to the Col reference.

Furthermore, the Ws genome has already been assembled as part of the 1001 Genomes project.....so, the dirty work has already been done

http://mus.well.ox.ac.uk/19genomes/fasta/