SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 177
Search took 0.02 seconds.
Search: Posts Made By: DZhang
Forum: Bioinformatics 11-12-2013, 10:34 AM
Replies: 11
Views: 7,877
Posted By DZhang
check here: https://usegalaxy.org/ Thank...

check here: https://usegalaxy.org/

Thank you,
Douglas
www.contigexpress.com
Forum: Bioinformatics 01-10-2013, 06:45 AM
Replies: 41
Views: 16,839
Posted By DZhang
I use picard (http://picard.sourceforge.net/) ...

I use picard (http://picard.sourceforge.net/)

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 11-08-2012, 06:20 AM
Replies: 13
Views: 5,654
Posted By DZhang
Hi rboettcher, According to my experience,...

Hi rboettcher,

According to my experience, yes, the numbering is according to the input order. Please verify with the developers directly, though.

You may want to analyze your data with a...
Forum: Bioinformatics 11-08-2012, 05:19 AM
Replies: 13
Views: 5,654
Posted By DZhang
rboettcher, are you referring to the Columns 2 &...

rboettcher, are you referring to the Columns 2 & 3 in the file? You can use simple scripts or even Excel to annotate the sample names (mostly likely in Column 3).

Best regards
Douglas...
Forum: Bioinformatics 09-07-2012, 03:00 PM
Replies: 4
Views: 3,869
Posted By DZhang
Do you want to simply remove the adapters or sort...

Do you want to simply remove the adapters or sort the reads out based on different adapters and then remove the adapters? Either way, please look into this tool:...
Forum: Bioinformatics 09-07-2012, 05:40 AM
Replies: 12
Views: 4,634
Posted By DZhang
Hi, I just want to add that we need to also...

Hi,

I just want to add that we need to also consider the potential sources of the duplication. Is it due to high coverage or PCR-amplification during library prep. It is never a clean cut but you...
Forum: Bioinformatics 09-04-2012, 06:16 AM
Replies: 2
Views: 1,888
Posted By DZhang
Hi RedMary, Did you inspect those regions in...

Hi RedMary,

Did you inspect those regions in a genome browser to make sure there were no reads mapped? If you may, please share a screen shot.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 09-03-2012, 07:29 AM
Replies: 8
Views: 3,462
Posted By DZhang
Hi Chris, Please read the paper on...

Hi Chris,

Please read the paper on MetaPhlAn. The authors screened for representative genes in each family/class. If you use a general database, I am not sure if the results are useful or not. I...
Forum: Bioinformatics 08-31-2012, 11:16 AM
Replies: 1
Views: 1,041
Posted By DZhang
Oscar, Take a look at this:...

Oscar,

Take a look at this: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990000/

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-31-2012, 06:36 AM
Replies: 8
Views: 3,462
Posted By DZhang
MetaPhlAn can do that. Best regards, ...

MetaPhlAn can do that.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-31-2012, 06:34 AM
Replies: 1
Views: 904
Posted By DZhang
There is only one version of hg19. All SNPs...

There is only one version of hg19. All SNPs (compared to hg19) are documented in SNP database.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-31-2012, 06:25 AM
Replies: 3
Views: 1,638
Posted By DZhang
Phil, For the first few question, you need a...

Phil,

For the first few question, you need a simple script to do the calculation based on the gene annotation. Or for a specific genome, all the ORF sequences may already exist in fasta, which...
Forum: Bioinformatics 08-31-2012, 06:10 AM
Replies: 2
Views: 1,538
Posted By DZhang
Can you share your commands? A little dot is what...

Can you share your commands? A little dot is what it takes to give you an empty file.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-31-2012, 06:06 AM
Replies: 2
Views: 928
Posted By DZhang
If the nature and time course of your...

If the nature and time course of your intervention are expected to generate new splicing variants or transcripts, you should merge both pre and post gtfs.

Best regards,
Douglas...
Forum: Bioinformatics 08-31-2012, 05:59 AM
Replies: 5
Views: 1,493
Posted By DZhang
Ng, If you have a BAM file aligned with...

Ng,

If you have a BAM file aligned with hg19, use any genome browser (e.g., IGV) and point it to the location for manual examination. I assume you can find the neighboring sequences of that...
Forum: Bioinformatics 08-31-2012, 05:44 AM
Replies: 1
Views: 1,860
Posted By DZhang
Dawe, Depending on what's downstream...

Dawe,

Depending on what's downstream experiment(s), you may focus on the overlapping 100 genes. (I assume you used the same fold/FDR criteria for both programs.) You may also plot them on a...
Forum: Bioinformatics 08-31-2012, 05:19 AM
Replies: 2
Views: 1,505
Posted By DZhang
Litc, RAD is strand-specific; it is...

Litc,

RAD is strand-specific; it is determined when the RAD adapter is ligated.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-31-2012, 05:13 AM
Replies: 15
Views: 4,318
Posted By DZhang
Hi John, Thank you for elaborating on this....

Hi John,

Thank you for elaborating on this. Please do inform us when your paper is out.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 03:35 PM
Replies: 3
Views: 1,433
Posted By DZhang
check this review:...

check this review: http://www.ncbi.nlm.nih.gov/pubmed?term=song%20albrechtsen
Hopefully it is helpful to you.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 02:04 PM
Replies: 8
Views: 3,462
Posted By DZhang
MetaPhlAn may be a right tool for this. ...

MetaPhlAn may be a right tool for this.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 01:53 PM
Replies: 2
Views: 1,012
Posted By DZhang
yes, WIG files omit positions with zero. ...

yes, WIG files omit positions with zero.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 01:50 PM
Replies: 3
Views: 1,150
Posted By DZhang
You need to write a script to process the file. ...

You need to write a script to process the file.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 09:36 AM
Replies: 1
Views: 1,104
Posted By DZhang
Hi, The samtools webpage has quite detailed...

Hi,

The samtools webpage has quite detailed explanation on the parameters. Here is the link: http://samtools.sourceforge.net/samtools.shtml.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 07:20 AM
Replies: 3
Views: 1,433
Posted By DZhang
gwilymh, GATK, samtools, and SOAPsnp are...

gwilymh,

GATK, samtools, and SOAPsnp are among my favorite tools for SNP analysis.

Best regards,
Douglas
www.contigexpress.com
Forum: Bioinformatics 08-29-2012, 07:15 AM
Replies: 5
Views: 1,658
Posted By DZhang
I believe it helps improve the results if you...

I believe it helps improve the results if you have a list of known indels.

Best regards,
Douglas
www.contigexpress.com
Showing results 1 to 25 of 177

 


All times are GMT -8. The time now is 12:24 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO