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Search: Posts Made By: cindylanzao
Forum: Bioinformatics 07-20-2017, 12:30 AM
Replies: 4
Views: 996
Posted By cindylanzao
Thanks for your nice method recommendation....

Thanks for your nice method recommendation. Another problem would be how to measure the heteroplasmy level of mitochondrial DNA. Thanks!
Forum: The Pipeline 07-16-2017, 07:42 PM
Replies: 1
Views: 4,290
Posted By cindylanzao
Mitochondrial heteroplasmy level detection

Hi, all

We are currently study mitochondrial genomics, however, find it confusing when try to detect the heteroplasmy level. Can some explain how to detect the heteroplasmy level? Some one said,...
Forum: Bioinformatics 07-16-2017, 07:33 PM
Replies: 4
Views: 996
Posted By cindylanzao
Yes, NGS data

Yes, NGS data
Forum: Bioinformatics 07-02-2017, 06:24 PM
Replies: 4
Views: 996
Posted By cindylanzao
Distinguish sequencing errors and real mutations in mitochondria data

Hi,all

We are searching a silico method to distinguish sequencing errors and real mutations from mitochondria sequencing data. Please do consider that the heteroplasmy in mitochondria. Thanks!
Forum: Bioinformatics 04-27-2017, 05:47 PM
Replies: 4
Views: 895
Posted By cindylanzao
Thanks Very Much

Thanks Very Much
Forum: Bioinformatics 04-24-2017, 11:28 PM
Replies: 4
Views: 895
Posted By cindylanzao
Thanks, could you explain a little bit of why...

Thanks, could you explain a little bit of why variants in these region could be false-positive?
Forum: Bioinformatics 04-24-2017, 05:21 PM
Replies: 4
Views: 895
Posted By cindylanzao
Remove SNP in segment duplication and repeat region

Hi,All

I am trying to detect somatic mutations in healthy people, I have searched some reference, however, both of the two detection method contains remove those variants in segment duplication...
Forum: Genomic Resequencing 04-23-2017, 05:02 PM
Replies: 0
Views: 1,239
Posted By cindylanzao
Somatic Mutation Amount

Hi,all
We are currently study the somatic mutations from blood sample from healthy individuals, and I am trying to build a pipeline to distinguish somatic mutations from germline mutations in these...
Forum: Bioinformatics 09-22-2015, 06:15 PM
Replies: 4
Views: 1,265
Posted By cindylanzao
Unhappy Thanks for your help, but the project is in a...

Thanks for your help, but the project is in a hurry, so I have decided to change to tophat as the aligner, and have deleted all the related output file from STAR.
Forum: Bioinformatics 09-20-2015, 09:17 PM
Replies: 0
Views: 643
Posted By cindylanzao
Smile Panel DNA data Remove Duplicates

Hi,all

We are doing panel data for variants calling and need to make it clear whether we should remove the duplicates with picard, I do not know the capture method, so, let us suppose there would...
Forum: Bioinformatics 09-20-2015, 05:56 PM
Replies: 4
Views: 1,265
Posted By cindylanzao
Question Thanks for your reply

Thanks for your kind reply Alex, I have checked the Log.progress.out, it contains nothing but the title after a whole night's running with only one sample with 12 thread. Do you have any other...
Forum: Bioinformatics 09-16-2015, 07:32 PM
Replies: 4
Views: 1,265
Posted By cindylanzao
Smile Computing time evaluate

Hi,all

I am doing RNA-seq alignment with STAR, my workstation is dual core(E5-2620v3), 12 thread in total, 64G RAM. I am running 9 mouse RNA-seq sample data(1GB/sample), parallelly, two days has...
Forum: RNA Sequencing 07-30-2015, 06:09 PM
Replies: 2
Views: 508
Posted By cindylanzao
Thanks, those website are really helpful!

Thanks, those website are really helpful!
Forum: RNA Sequencing 07-30-2015, 01:17 AM
Replies: 2
Views: 508
Posted By cindylanzao
Paired RNA-seq data for Arabidopsis

Hi, all

I have just built a RNA-seq pipeline for Arabidopsis, and do need a set of paired sample of RNA-seq PE or SE data for Arabidopsis, can someone tell me where can I find this kind of data....
Forum: Bioinformatics 07-22-2015, 06:46 PM
Replies: 0
Views: 604
Posted By cindylanzao
Smile DEXSeqHTML() function from DEXSeq fails to generate the complete report

I followed the official instructions on DEXSeq biocondoctor package(data from pasilla package as suggested), and wants to generate the HTML report with the DEXSeqHTML function as suggested in the...
Forum: Ion Torrent 11-10-2013, 03:55 PM
Replies: 7
Views: 4,605
Posted By cindylanzao
Thanks to all you guys offering me help!

Thanks to all you guys offering me help!
Forum: Ion Torrent 11-08-2013, 08:40 PM
Replies: 7
Views: 4,605
Posted By cindylanzao
Smile Can someone offers me a guidance of Torrent suite?

I read the Readme, but I cannot find the guidance on how to use this software apart from the guidance of installing this software. Where can I get the manual? Thanks
Forum: Ion Torrent 11-08-2013, 04:02 AM
Replies: 7
Views: 4,605
Posted By cindylanzao
Ion Proton data analysis software

I am a newbie in this field, can anyone give me a list on the name of the current available software for Ion Proton data analysis?References recommendation is also welcome.Thank you guys so much!:)
Forum: General 11-06-2012, 12:37 PM
Replies: 1
Views: 859
Posted By cindylanzao
Bioperl beginner's program

!usr/bin/perl -w

use Bio::DB::GenBank;
use Bio::Restriction::EnzymeCollection;
use Bio::Restriction::Analysis;
my $gb=new Bio::DB::GenBank();
my $seq=$gb->getSeqbyacc('AF303112');
print...
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