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Search: Posts Made By: Gangcai
Forum: Bioinformatics 07-07-2011, 03:42 AM
Replies: 9
Views: 5,775
Posted By Gangcai
Hi Simon, I have tried the deve version of...

Hi Simon,
I have tried the deve version of DESeq. The number of significant genes drop quite a lot. It does look better comparing with previous result. But still have some genes have high...
Forum: Bioinformatics 07-07-2011, 02:24 AM
Replies: 9
Views: 5,775
Posted By Gangcai
Hi Simon, Thanks for your quick reply. One...

Hi Simon,
Thanks for your quick reply. One more question about installation of the devel DESeq.
I have downloaded the newest version of Biobase from bioconductor, but DESeq require even advanced...
Forum: Bioinformatics 07-07-2011, 12:39 AM
Replies: 9
Views: 5,775
Posted By Gangcai
Dear Simon, I have quite similar problem for...

Dear Simon,
I have quite similar problem for the significant genes detected by DESeq and edgeR. Both of them output some significant candidates which have quite large variation within groups. Such...
Forum: Literature Watch 05-26-2011, 01:51 PM
Replies: 7
Views: 8,482
Posted By Gangcai
Has anybody tried this method/software?

Has anybody tried this method/software?
Forum: Bioinformatics 03-04-2011, 12:52 AM
Replies: 7
Views: 4,951
Posted By Gangcai
Does anybody know how cuffdiff assign p value?

Does anybody know how cuffdiff assign p value?
Forum: General 01-24-2011, 03:18 AM
Replies: 18
Views: 7,109
Posted By Gangcai
That means the wig file is too large to be...

That means the wig file is too large to be submitted to UCSC. You can try to convert wig file to bigwig by the wigToBigWig program provided by UCSC. Hope it works.
Forum: General 01-21-2011, 07:05 AM
Replies: 18
Views: 7,109
Posted By Gangcai
Just upload both of them to UCSC (submit one file...

Just upload both of them to UCSC (submit one file each time), then you can see both of them on Genome Browser.
Forum: Bioinformatics 01-21-2011, 03:31 AM
Replies: 2
Views: 4,126
Posted By Gangcai
Unclear about Indels calling in samtools pileup file

Hi everyone,
Has anybody solved the problem already? I also meet the same problem. In my case,
I want to know if an Indel is homozygous or heterzygous. The pileup file(from Sanger SNP pileup...
Forum: Bioinformatics 12-19-2010, 02:52 AM
Replies: 4
Views: 5,345
Posted By Gangcai
I met the same problem. Is this problem solved...

I met the same problem. Is this problem solved for you?
Forum: Bioinformatics 11-16-2010, 10:26 PM
Replies: 2
Views: 2,450
Posted By Gangcai
I have fixed the preprocessing step, but...

I have fixed the preprocessing step, but "'original_BS' is not defined" error still exist...
Forum: Bioinformatics 11-16-2010, 02:39 AM
Replies: 2
Views: 2,450
Posted By Gangcai
I have re-checked the reference preprocessing,...

I have re-checked the reference preprocessing, there is one error I missed:
"Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation."
Forum: Bioinformatics 11-16-2010, 12:28 AM
Replies: 2
Views: 2,450
Posted By Gangcai
BS_Seeker 'original_BS' is not defined

Hi everybody,
I am using BS_Seeker(http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html ) to process the bisulfite converted sequencing data.
There is no trouble for genome preprocessing...
Forum: Bioinformatics 08-05-2010, 05:57 PM
Replies: 6
Views: 2,704
Posted By Gangcai
I am trying to use scripture now. Yes , it needs...

I am trying to use scripture now. Yes , it needs some pre-processing of tophat output files, including combining, sorting, and indexing. I have just finished the pre-processing right now.
Forum: Bioinformatics 08-04-2010, 06:02 PM
Replies: 0
Views: 2,694
Posted By Gangcai
Question strange bowtie index building and mapping problem

Hello everyone,
I have met a quite strange problem when running bowtie for my SOLID sequencing result.
I have succeeded to build bowtie colorspace index for chimpanzee whole genome, but when...
Forum: Bioinformatics 08-03-2010, 01:19 AM
Replies: 6
Views: 2,704
Posted By Gangcai
You can try scripture for assembly also :...

You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/
Forum: Bioinformatics 03-16-2010, 01:05 AM
Replies: 2
Views: 1,932
Posted By Gangcai
It's human. And the blat result is : ...

It's human.
And the blat result is :
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN...
Forum: Bioinformatics 03-12-2010, 11:23 PM
Replies: 2
Views: 1,932
Posted By Gangcai
Redundant(?) report problem in tophat .sam file?

Hi everyone,
I have checked the tophat sam file from tophat1.0.11, and found one reads have been reported twice(same genome location but different optional fields). Why two different mismatch(...
Forum: Bioinformatics 03-12-2010, 11:13 PM
Replies: 2
Views: 3,757
Posted By Gangcai
What does NS:i:1 means in the .sam format files?

Hi everyone,
I have the .sam file from tophat, and the last optional fields is NS:i:1. I have checked the sam manual, but cannot find NS Tag

(also for XS (XS:A:-), but can be found in cufflinks...
Forum: Bioinformatics 03-11-2010, 05:28 PM
Replies: 4
Views: 3,776
Posted By Gangcai
I have send you the email, please check it~~

I have send you the email, please check it~~
Forum: Bioinformatics 03-11-2010, 07:12 AM
Replies: 4
Views: 3,776
Posted By Gangcai
MRNM problem for the .sam output file of tophat

Hi everyone,
MRNM is the 7th field in the sam file. I got the sam output from tophat, it seems that the MRNM is not correct in my case.

$ grep "HWI-EAS244_1_1_116_848_845_0_1_12496949"...
Forum: Bioinformatics 03-03-2010, 05:21 PM
Replies: 11
Views: 8,543
Posted By Gangcai
you can modify the tophat bin file

The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After...
Forum: Bioinformatics 02-28-2010, 07:18 PM
Replies: 11
Views: 8,543
Posted By Gangcai
I also have a quite similar question: How to set...

I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?
Forum: Bioinformatics 01-28-2010, 08:02 PM
Replies: 4
Views: 5,307
Posted By Gangcai
How does inner distances(--mate-inner-dist and --mate-std-dev) work in tophat?

I am confused about the inner distance setting. From the manual file, it should be set to (fragementlength-2*readslength , eg: 300-2*50=100). But if the distance counting is based on genome...
Forum: Bioinformatics 01-28-2010, 06:51 PM
Replies: 0
Views: 1,864
Posted By Gangcai
Smile Another assembly tools: LOCAS (Has anyone tried already?)

I have found another assembly tools LOCAS (http://www-ab.informatik.uni-tuebingen.de/software/locas ), but it seems there is only binary files(Redhat, 64-bit). Will they provide the source code in...
Forum: Bioinformatics 01-16-2010, 07:43 PM
Replies: 4
Views: 2,316
Posted By Gangcai
Thanks for your reply! So this means for 0-base...

Thanks for your reply!
So this means for 0-base chromosome postion, the start part is included. But for 1-based chromosome position, the end part is included(Just treat as 1-based).
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