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Search: Posts Made By: jay2008
Forum: Bioinformatics 02-16-2016, 01:27 PM
Replies: 5
Views: 1,155
Posted By jay2008
thanks, the code is from supplementary 2....

thanks, the code is from supplementary 2. actually, i try to do it work in current DESeq version.
can anyone else help this issue?
Forum: Bioinformatics 02-16-2016, 01:15 PM
Replies: 3
Views: 2,061
Posted By jay2008
thanks, i have already installed R-2.11version. I...

thanks, i have already installed R-2.11version. I tried install individual package, but it is so hard to find all dependencies with correct version.
Forum: Bioinformatics 02-16-2016, 03:58 AM
Replies: 5
Views: 1,155
Posted By jay2008
I am going to investigate the difference between...

I am going to investigate the difference between DESeq and DESeq2. the reason is that I can better understand the advantages of DESeq2 by reading, testing original DESeq.
you are right, as a user,...
Forum: Bioinformatics 02-16-2016, 12:11 AM
Replies: 5
Views: 1,155
Posted By jay2008
DESeq baseVarFunc is not working

can you help me to make function "baseVarFunc" below (from supplementary 2 of DESeq paper) work?
I got error:
Error in baseVarFunc(cdsFly, "A")(10^xg) : could not find function "rvf"

here is the...
Forum: Bioinformatics 02-15-2016, 04:19 PM
Replies: 3
Views: 2,061
Posted By jay2008
how to install previous released bioconductor

Hello,
I can find bioconductor old version such as https://www.bioconductor.org/packages/2.6/BiocViews.html#___Software
but I could not find how to install it.
can anyone please tell me how to...
Forum: Bioinformatics 02-14-2016, 03:31 PM
Replies: 3
Views: 1,799
Posted By jay2008
thanks for your reply. there is no archive in...

thanks for your reply.
there is no archive in bioconductor(http://bioconductor.org/packages/release/bioc/html/DESeq.html). it is be great appreciated if you can tell me how to get it.
I checked...
Forum: Bioinformatics 02-14-2016, 12:29 AM
Replies: 3
Views: 1,799
Posted By jay2008
comparison of DESeq, DESeq2 and edgeR

Hello,
I am going to compare DESeq, DESeq2 and edgeR with comprehensive data sets. could you provide source code for DESeq 1.1 12 version?

kind regards
Jay
Forum: Bioinformatics 09-25-2014, 07:11 PM
Replies: 0
Views: 741
Posted By jay2008
p-val in DESeq

Eq. 12 (page 3) in DESeq paper seem to be incorrect, because it is "pooled mean", but the formula is sum. I guess right hand need to be divided by (m_A + m_B).
could anyone clarify it?
is the s_j...
Forum: Bioinformatics 08-12-2013, 10:34 PM
Replies: 4
Views: 1,538
Posted By jay2008
bam file can be sorted in two ways: coordinate...

bam file can be sorted in two ways: coordinate and queryname (sorted by read name). bam.query is based on coordinate. I can not find any APIs for bam file sorted by queryname. I guess there should be...
Forum: Bioinformatics 08-11-2013, 04:22 PM
Replies: 3
Views: 1,192
Posted By jay2008
thanks. I got it. if bam file is sorted, using...

thanks. I got it.
if bam file is sorted, using picard API, searching by chromosome coordinate is very quick. what picard API should I use to search by read name (for example,...
Forum: Bioinformatics 08-11-2013, 06:15 AM
Replies: 3
Views: 1,192
Posted By jay2008
tophat marking "read in a proper pair" wrongly

Hi
I have a paired end reads below mapping to genome perfectly, but tophat (ver 2.0.4) mark "not mapped in proper pair". flag = 161 and 81. can anyone explain it?
...
Forum: Bioinformatics 08-10-2013, 04:57 AM
Replies: 4
Views: 1,538
Posted By jay2008
I meant what the API in picard can be used.

I meant what the API in picard can be used.
Forum: Bioinformatics 07-08-2013, 06:41 AM
Replies: 4
Views: 1,538
Posted By jay2008
query read by read name

Hello,
I am using picard library in java.
is it possible to make query for a specific readname in a bam file?

thanks
Yu
Forum: Bioinformatics 02-22-2013, 05:58 AM
Replies: 3
Views: 1,653
Posted By jay2008
tophat generates XS tag. we should not give...

tophat generates XS tag. we should not give library type to cufflinks command. is it right?
in other words, if we use fr-firststrand library in tophat, what will happen if we put fr-secondstrand...
Forum: Bioinformatics 02-22-2013, 12:34 AM
Replies: 3
Views: 1,653
Posted By jay2008
why tophat has library type for paired end?

hello,
unlike cufflinks,
tophat maps reads to genome without considering strand.
why does tophat need to set library type?

thanks
Yu
Forum: Bioinformatics 01-25-2013, 03:21 PM
Replies: 4
Views: 2,461
Posted By jay2008
RNAfold is most time-consuming task in predicting...

RNAfold is most time-consuming task in predicting miRNAs from deep sequencing. All current predicting tools miRDeep, miRTRAP, MIReNA, miRDeep* and etc. use similar RNA secondary structure prediction...
Forum: Bioinformatics 01-20-2013, 11:38 PM
Replies: 5
Views: 5,035
Posted By jay2008
hi sgombar, miRdeep* may help you. ...

hi sgombar,
miRdeep* may help you.
https://sourceforge.net/projects/mirdeepstar/
Forum: Bioinformatics 01-13-2013, 02:43 PM
Replies: 0
Views: 2,667
Posted By jay2008
how to close index file (xxx.bai) in picard

hi,
we can open indexed bam file with:
File bam, index,
SAMFileReader reader = new SAMFileReader(bam, index);
or
SAMFileReader reader = new SAMFileReader(bam);

but after
reader.close();
Forum: Bioinformatics 12-18-2012, 01:43 AM
Replies: 4
Views: 3,888
Posted By jay2008
you may use miRDeep* where the genomic mapping is...

you may use miRDeep* where the genomic mapping is embedded.
http://nar.oxfordjournals.org/content/early/2012/12/04/nar.gks1187.abstract
Forum: Bioinformatics 11-28-2012, 12:12 AM
Replies: 0
Views: 1,496
Posted By jay2008
how to know whether a bam file is strand specific?

Hello,
can anyone tell me how to check whether a bam file is from a strand-specific sequecening or not?

for indivial read we can get
!re.getReadNegativeStrandFlag() &&...
Forum: Bioinformatics 11-19-2012, 12:55 PM
Replies: 0
Views: 753
Posted By jay2008
SnappyError in picard

Hello,

when I use picard 1.46, I got an error. it seems picard uses Snappy class.
can anyone tell me how to solve the problem?
thanks
Yu



Exception in thread "main"...
Forum: Bioinformatics 11-19-2012, 12:28 PM
Replies: 9
Views: 12,664
Posted By jay2008
I have another problem using picard: can anyone...

I have another problem using picard: can anyone tell me how to get org.xerial.snappy?


Exception in thread "main" java.lang.NoClassDefFoundError: org/xerial/snappy/SnappyError
at...
Forum: Bioinformatics 10-10-2012, 03:16 PM
Replies: 0
Views: 895
Posted By jay2008
is it bug in cufflinks?

hello,
I run cufflinks and got the following transcripts from transcript.gtf:
chrX Cufflinks transcript 107821319 107840299 1000 + . gene_id "CUFF.33619";transcript_id "CUFF.33619.1"; FPKM...
Forum: Bioinformatics 09-28-2012, 05:32 PM
Replies: 8
Views: 3,295
Posted By jay2008
I am tring to use miRTRAP. when I set...

I am tring to use miRTRAP. when I set "repeatRegionsFile" to an empty file. I got error :
could not open 16714.
is "repeatRegionsFile" necessary? for human genome, how can I get...
Forum: Bioinformatics 06-23-2012, 04:45 AM
Replies: 8
Views: 3,295
Posted By jay2008
there are several tool to predict miRs such as...

there are several tool to predict miRs such as miRDeep, MIReNA. what is the advantages for different miR prediction tools?

Yu
Showing results 1 to 25 of 44

 


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