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Forum: Bioinformatics 06-04-2013, 03:50 PM
Replies: 11
Views: 21,837
Posted By camelbbs
I think sam files can be merged as : cat sam1...

I think sam files can be merged as :
cat sam1 sam2 > sam

and then sort it.

Am i right?
Forum: Bioinformatics 02-01-2013, 10:06 AM
Replies: 3
Views: 1,265
Posted By camelbbs
Hi Alejandro, I suddenly think that in...

Hi Alejandro,

I suddenly think that in DESeq, do I also need to import two conditions each time to do the estimatesizefactor and estimatedispersions?
can I import all conditions (>=3) together,...
Forum: Bioinformatics 01-11-2013, 07:50 PM
Replies: 3
Views: 1,265
Posted By camelbbs
I see, Thanks!

I see, Thanks!
Forum: Bioinformatics 01-09-2013, 10:34 AM
Replies: 3
Views: 1,265
Posted By camelbbs
how to specify samples for comparison in dexseq

Hi all,

I want to ask how to specify conditions for DEU detection in DEXSeq.

I see in DESeq, after I do estimateDispersion, I can use

res<-nbinomTest(cds,"sample1","sample2")

to specify...
Forum: Bioinformatics 11-19-2012, 02:08 PM
Replies: 14
Views: 6,288
Posted By camelbbs
Smile Hi Wolfgang, While I comment the line: ...

Hi Wolfgang,

While I comment the line:

if( nrow(mm) <= ncol(mm) )
stop( "Underdetermined model; cannot estimate dispersions. Maybe replicates have not been properly specified." )

and run...
Forum: RNA Sequencing 11-14-2012, 04:29 PM
Replies: 2
Views: 3,583
Posted By camelbbs
Thanks, I have got it.

Thanks, I have got it.
Forum: Bioinformatics 11-13-2012, 08:49 AM
Replies: 14
Views: 6,288
Posted By camelbbs
Hi Wolfgang, Thanks very much. But while I...

Hi Wolfgang,
Thanks very much. But while I downloaded the core_function.R and modified it, I get an error to load it:

> source("C:\\Users\\cjhe\\Desktop\\dexseq\\core_functions.R")
Error in...
Forum: Bioinformatics 11-12-2012, 09:49 PM
Replies: 14
Views: 6,288
Posted By camelbbs
Wink HI, I want to ask how to remove this line....

HI,

I want to ask how to remove this line. Since where I can find the raw scripts in R installation folders.

Thanks..
Forum: Bioinformatics 11-11-2012, 10:17 AM
Replies: 24
Views: 16,174
Posted By camelbbs
difference between htseq-count and bedtools multicov

Hi,

Anyone have used htseq-count and bedtools multicov, I use both them to get the read counts for ref genes. But I got very different read counts between them. Which one is more common..
...
Forum: RNA Sequencing 11-09-2012, 06:04 PM
Replies: 2
Views: 3,583
Posted By camelbbs
Question of using DESeq for non-replicate samples

HI.

I've tried the package DESeq and want to apply in our datasets: two samples without replicates.

I first summarized the counts in a table:
brain liver
uc001aaa.3 0 0...
Forum: RNA Sequencing 10-16-2012, 09:07 AM
Replies: 2
Views: 1,380
Posted By camelbbs
i don't know. But RNAseq will also give many...

i don't know. But RNAseq will also give many reads at annotated intron regions, right?
Forum: RNA Sequencing 10-11-2012, 03:06 PM
Replies: 2
Views: 1,380
Posted By camelbbs
a question about rpkm calculation

Hi
I want to ask an important question in RNAseq:

why I need to include the reads in intron while i calculate the RPKM for one gene or transcript/isoform.

I think it is necessary to exclude...
Forum: RNA Sequencing 09-17-2012, 11:31 AM
Replies: 5
Views: 1,786
Posted By camelbbs
I think bed12 file show the right thing. thanks....

I think bed12 file show the right thing. thanks. Can you explain what is the change in bed12 file comparing to bed.

bed file:

chr1 14396 14517 DJG84KN1:219:D0R66ACXX:7:1213:7112:52613/2...
Forum: RNA Sequencing 09-17-2012, 11:25 AM
Replies: 5
Views: 1,786
Posted By camelbbs
Thanks. I just curious while I view bed and bam...

Thanks. I just curious while I view bed and bam files in IGV, they show difference. bed file have coverage in intron region, but not in bam.
Forum: RNA Sequencing 09-15-2012, 10:16 AM
Replies: 5
Views: 1,786
Posted By camelbbs
Thanks, and how to view bed12 files in IGV?

Thanks, and how to view bed12 files in IGV?
Forum: RNA Sequencing 09-13-2012, 08:18 PM
Replies: 5
Views: 1,786
Posted By camelbbs
writing script to convert bam to bed

Hi,
I want to ask if anyone write a script to convert bam to bed.

I tried bamtools bamtobed but while i import the result bed files to IGV, i see it is very different to the bam files.

So I...
Forum: Bioinformatics 06-18-2012, 02:09 PM
Replies: 1
Views: 1,505
Posted By camelbbs
the insert size in rnaseq

HI I have paired-end rnaseq data in sam files like this:

...
Forum: RNA Sequencing 06-15-2012, 07:31 PM
Replies: 0
Views: 913
Posted By camelbbs
a question about gap

Hi,

I have 3 questions about RNA-seq analysis:

1. How do I know the inner distance between two pair-end seq? If the sequencing company don't tell me that, how can I find it.

2. If the inner...
Forum: De novo discovery 06-15-2012, 10:49 AM
Replies: 9
Views: 2,605
Posted By camelbbs
Well..I'll try it. Thanks a lot!

Well..I'll try it. Thanks a lot!
Forum: De novo discovery 06-15-2012, 10:15 AM
Replies: 9
Views: 2,605
Posted By camelbbs
Smile do you have an idea about compare the two...

do you have an idea about compare the two genomes? BLAST? Thanks!
Forum: De novo discovery 06-14-2012, 05:11 PM
Replies: 9
Views: 2,605
Posted By camelbbs
Because we do PCR, race, etc to get the gene of...

Because we do PCR, race, etc to get the gene of that fish we want, tired of experiment with very limited info, we sequenced that fish and hope it can help improve the experiment. But now for the...
Forum: De novo discovery 06-14-2012, 03:38 PM
Replies: 9
Views: 2,605
Posted By camelbbs
It's a kind of fish. So it's useless?

It's a kind of fish. So it's useless?
Forum: De novo discovery 06-14-2012, 03:30 PM
Replies: 9
Views: 2,605
Posted By camelbbs
ask for idea about de novo genome

Recently we sequenced an uncommon animal genome. I want to ask what can we do to that?
Call SNP/Indel? seems can't, because there is no reference.

compare with other species? or do comparative...
Forum: RNA Sequencing 05-20-2012, 12:13 PM
Replies: 0
Views: 995
Posted By camelbbs
cuffmerge question

HI,

I want to ask what is the differece between put hg19.gtf in -g option and put hg19.gtf in the gtf list:

cuffmerge -g hg19.gtf list.txt
cuffmerge list.txt (including hg19.gtf)

I run...
Forum: Bioinformatics 11-17-2011, 09:06 AM
Replies: 3
Views: 2,964
Posted By camelbbs
There is no explanation for this file in cuffdiff...

There is no explanation for this file in cuffdiff documents. I hope someone can add it.
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