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Search: Posts Made By: yuelics
Forum: Bioinformatics 07-24-2012, 06:21 PM
Replies: 4
Views: 1,280
Posted By yuelics
Sorry I found it ... it is the "-sp" option in...

Sorry I found it ... it is the "-sp" option in the HPeak.pl script
Forum: Bioinformatics 07-24-2012, 06:19 PM
Replies: 4
Views: 1,280
Posted By yuelics
Thanks Peter! I downloaded the package and see 3...

Thanks Peter! I downloaded the package and see 3 new scripts: chiphmm_mm9 hmmminus_mm9 peakann_mm9.pl

did you how to make HPeak to run on the "mm9" but not the "hg19" scripts? From the manual,...
Forum: Bioinformatics 04-23-2012, 04:39 PM
Replies: 2
Views: 3,739
Posted By yuelics
thanks. GenomicRanges seems to be able to do sth...

thanks. GenomicRanges seems to be able to do sth similar and but will need to dig around a bit.
Forum: Bioinformatics 04-23-2012, 03:28 PM
Replies: 2
Views: 3,739
Posted By yuelics
Use BedTools in R package

Dear friends and colleagues,

I wonder if anyone knows how to build an R package that can compile BedTools c source code as there are quite a few functions in BedTools that are very useful to my R...
Forum: Bioinformatics 04-13-2012, 01:27 PM
Replies: 1
Views: 1,608
Posted By yuelics
Same question here.

Same question here.
Forum: Bioinformatics 04-04-2012, 04:30 AM
Replies: 5
Views: 3,652
Posted By yuelics
Hi Rocketknight, Thanks a lot for your...

Hi Rocketknight,

Thanks a lot for your reply. I actually managed to get Bowtie working on the short 7mer with a few additional options. The tricky thing of writing a script to do it is that the...
Forum: Bioinformatics 04-01-2012, 06:51 AM
Replies: 5
Views: 3,652
Posted By yuelics
minimal read length accepted by Bowtie

Hi all,

I wonder if anyone knows the minimal read length accepted by Bowtie. Basically, I have a set of short motif sequences (7mers) and want to see where they map to the mouse reference genome....
Forum: Bioinformatics 08-16-2011, 06:06 PM
Replies: 4
Views: 1,280
Posted By yuelics
how to make HPeak work for non-human ChIPSeq and split out p-values ??

HPeak is a very nice HMM-model-based peak calling program. However, the current version HPeak 2.1 has two big problems: 1. only works for human genome; 2. output containing no p-value.

I wonder if...
Forum: Bioinformatics 08-05-2011, 05:48 AM
Replies: 5
Views: 8,619
Posted By yuelics
I have a related question. How can I make bowtie...

I have a related question. How can I make bowtie to output both sam and bowtie format without running it twice with two different output options? Some downstream programs need bowtie format, but some...
Forum: RNA Sequencing 08-01-2011, 04:39 PM
Replies: 2
Views: 3,060
Posted By yuelics
I would like that too. But it seems currently...

I would like that too. But it seems currently tophat is missing lots of useful options in bowtie such as "--trim", "--best", "--tryhard" etc. What bugs me the most is that Tophat returns ALL the...
Forum: Introductions 07-29-2011, 04:50 AM
Replies: 3
Views: 4,806
Posted By yuelics
Thanks westerman. Based on your analysis, if we...

Thanks westerman. Based on your analysis, if we know the transcripts along the genome, then it is better to use read coverage.

In de novo approach, where a sliding window of fixed size is used,...
Forum: Bioinformatics 07-27-2011, 04:48 AM
Replies: 0
Views: 2,157
Posted By yuelics
Quantification: count reads or count base pairs?

Hi all,

I am new to the field. Here is a silly question:

For quantification of defined genomic regions (let it be genes, windows of a fixed size, etc) based on sequencing data, why do people...
Forum: Introductions 07-26-2011, 05:48 PM
Replies: 3
Views: 4,806
Posted By yuelics
count reads or count base-pairs

Hi all,

I am new to the field. Here is a silly question:

For quantification of defined genomic regions (let it be genes, windows, etc) based on sequencing data, why do people rarely count...
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