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Forum: Bioinformatics 10-26-2010, 02:15 AM
Replies: 40
Views: 15,428
Posted By qqcandy
Does Dindel also do anchor-split mapping, as...

Does Dindel also do anchor-split mapping, as Pindel? Or the indels discovered by Dindel has to be supported by at least one mappable reads by the aligners, such as bwa/novoalign?
Forum: Bioinformatics 08-05-2010, 01:43 AM
Replies: 5
Views: 5,227
Posted By qqcandy
I have the same question...

I have the same question...
Forum: Bioinformatics 07-14-2010, 06:00 AM
Replies: 1
Views: 2,862
Posted By qqcandy
Picard MergeSamFile Memory Increase

Does anyone know how I can increase the memory allowance of Picard MergeSamFile? The current one always use around 2 to 3G, no matter how much memory the machine actually has... And I can't find any...
Forum: Bioinformatics 06-30-2010, 12:00 AM
Replies: 7
Views: 4,161
Posted By qqcandy
Thanks a lot! I think we've got a consensus for...

Thanks a lot! I think we've got a consensus for option 2 :)
Forum: Bioinformatics 06-25-2010, 06:56 AM
Replies: 7
Views: 4,161
Posted By qqcandy
novoalign multi-threading or para-processing?

I have a question about para-processing of novoalign:

If we have 1 node with 8 cores and 8 lanes of Illuimina data to process, there are two ways to run it:

1. assign 1 lane of data to each...
Forum: Bioinformatics 01-19-2010, 02:58 PM
Replies: 14
Views: 22,721
Posted By qqcandy
Yes, except they knew they probably had only one...

Yes, except they knew they probably had only one mutation to look for and that mutation is probably in all disease samples; while in our case, there are for certain more than one somatic mutations in...
Forum: Bioinformatics 01-19-2010, 08:40 AM
Replies: 14
Views: 22,721
Posted By qqcandy
Smile Thank you for the suggestion. Could you explain...

Thank you for the suggestion. Could you explain why filter out SNP from large studies? They are more likely to include somatic mutations, or they have little annotation? Thanks
Forum: Bioinformatics 01-18-2010, 11:45 AM
Replies: 14
Views: 22,721
Posted By qqcandy
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book...

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq&part=Submit.Submitting_Various_D

"""
Q: Can we submit SNPs that might be somatic mutations? Problem is, we don’t know which are...
Forum: Bioinformatics 01-18-2010, 11:42 AM
Replies: 14
Views: 22,721
Posted By qqcandy
Somatic Mutations in dbSNP

We are looking for somatic mutations in tumor by exon sequencing with paired normal samples. Our original plan is to sequence 20 tumor samples and filter out polymorphisms/mutations in dbSNP129. Then...
Forum: Bioinformatics 10-03-2008, 02:31 PM
Replies: 14
Views: 8,755
Posted By qqcandy
Just found this which may be useful to people who...

Just found this which may be useful to people who are interested in SNP call using short reads data:

Conversion of Novoalign to Maq's .map format (calling SNPs and Indels)
...
Forum: Bioinformatics 10-03-2008, 02:29 PM
Replies: 14
Views: 8,755
Posted By qqcandy
For more sophisticated SNP detection (although in...

For more sophisticated SNP detection (although in most cases not needed), it may be useful to have the quality score for each call. E.g. for position 33133, what is the score for the one C, what are...
Forum: Bioinformatics 10-03-2008, 12:34 PM
Replies: 14
Views: 8,755
Posted By qqcandy
Thanks a lot for the suggetions! Now I...

Thanks a lot for the suggetions!

Now I understand that getting the alignment while assessing SNP is not a good idea. It is better to have the reads aligned first, then take all the reads that...
Forum: Bioinformatics 10-03-2008, 07:18 AM
Replies: 14
Views: 8,755
Posted By qqcandy
Thank you for your reply! Your first...

Thank you for your reply!

Your first understanding is right -- mapping reads in paired way, then using the mapping results to extract SNP.

For MAQ, does it do mapping first and then SNP...
Forum: Bioinformatics 10-01-2008, 05:06 PM
Replies: 14
Views: 8,755
Posted By qqcandy
SNP/Mutation Detection Using Illumina Paired-end Data

This website is really useful and I've found answers to many questions I had by just reading the existing threads.

However, I have not found answer to this question -- what program/pipeline I...
Forum: General 10-01-2008, 04:58 PM
Replies: 0
Views: 2,470
Posted By qqcandy
SNP/mutation Using Illumina Paired-end Data

http://seqanswers.com/forums/showthread.php?p=1732#post1732
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