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Forum: Bioinformatics 04-17-2014, 07:02 PM
Replies: 1
Views: 1,124
Posted By alittleboy
Smile RNA-Seq sequencing depth information from NCBI

I am working on several datasets downloaded from NCBI SRA. For example, the zebrafish dataset accessible from:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44233

is used for my...
Forum: Bioinformatics 03-13-2014, 10:22 PM
Replies: 1
Views: 1,205
Posted By alittleboy
Smile understand the "left" and "right" outputs from NCBI data

I am trying to understand what do the columns mean for a sequencing dataset that I downloaded from NCBI. The link to the page is http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49372, and I...
Forum: Bioinformatics 03-05-2014, 10:14 PM
Replies: 1
Views: 1,049
Posted By alittleboy
Smile Finding RNA-Seq datasets across species

I plan to examine several RNA-Seq datasets (say 5-6), and hopefully there have the following characteristics:

1. Different species: human, mouse, zebrafish, yeast, arabidopsis, etc.
2. With...
Forum: Bioinformatics 08-14-2013, 07:13 AM
Replies: 4
Views: 1,283
Posted By alittleboy
Thank you alexdobin for the suggestions! Can I...

Thank you alexdobin for the suggestions! Can I know how you solved this problem (i.e. modifications of the GTF file...)? :)
Forum: Bioinformatics 08-14-2013, 06:52 AM
Replies: 4
Views: 1,283
Posted By alittleboy
a question in using Flux Simulator

I am using Flux Simulator to simulate RNA-Seq experiment, and after running

flux-simulator -p /HS_simu1.par

I got the following error message:

[ERROR] Error while preparing sequences:...
Forum: Bioinformatics 07-25-2013, 12:18 PM
Replies: 0
Views: 947
Posted By alittleboy
distribution of number of reads mapped to a union-transcript

If we consider all isoforms of a gene, and construct a "union transcript", then we can calculate the number of reads uniquely mapped to each exon of the union transcript. My question is, what is the...
Forum: Bioinformatics 07-24-2013, 05:33 AM
Replies: 4
Views: 2,744
Posted By alittleboy
Well, I guess not, but I think a histogram like...

Well, I guess not, but I think a histogram like what the link points to should be more reasonable... What do you think? Did you ever plot the p-value histograms for the DE test results? THANKS :)
Forum: Bioinformatics 07-22-2013, 01:41 PM
Replies: 4
Views: 2,744
Posted By alittleboy
pattern of p-values for DE testing for RNA-Seq data

I have a very general question on roughly checking the results of DE tests for RNA-Seq data.

After a proper comparison of a control and treatment group using, say, edgeR, DESeq, etc., we can plot...
Forum: Bioinformatics 07-15-2013, 10:09 AM
Replies: 5
Views: 2,919
Posted By alittleboy
Hi @areyes: Thanks so much! I tried that on...

Hi @areyes:

Thanks so much! I tried that on my own ExonCountSet object, and it works well. I personally think that exonsByTranscript is more informative as I can pass a particular transcript name...
Forum: Bioinformatics 07-12-2013, 10:24 AM
Replies: 5
Views: 2,919
Posted By alittleboy
Hi @areyes: Would you please give me some...

Hi @areyes:

Would you please give me some examples on how to get the real exons from the fData(ExonCountSet_obj) output (which contains exon bins start and end information)? Thanks a lot!
Forum: Bioinformatics 07-12-2013, 10:02 AM
Replies: 2
Views: 1,726
Posted By alittleboy
Dear Wolfgang: Thank you so much for your...

Dear Wolfgang:

Thank you so much for your insights! Yes, I strongly agree that if we know the data-generating truth, then there should be a consensus on which DE test tool is best.

Because I am...
Forum: Bioinformatics 07-11-2013, 10:15 AM
Replies: 2
Views: 1,726
Posted By alittleboy
benchmarking tools for evaluating methods for differential exon usage

Dear All:

I am recently doing methodological comparisons among different tools for testing differential exon usage (DEU), and this is a general question about how we evaluate the many approaches...
Forum: Bioinformatics 07-10-2013, 11:29 AM
Replies: 2
Views: 2,577
Posted By alittleboy
Hi @space_monkey: Here are some comments --...

Hi @space_monkey:

Here are some comments -- I contact the authors and gave my partial outputs, and the reply is below:

It does look like a headers mismatch then. Your BAM file contains "chr"...
Forum: Bioinformatics 07-08-2013, 07:16 AM
Replies: 5
Views: 2,919
Posted By alittleboy
Question Comparing DEXSeq counting bin and real exons

Hi All:

I use DEXSeq for detecting differential exon usage (DEU), and the results seem to be good. One thing I am not sure is that, I know which gene has DEU, and I know which "exonic region...
Forum: Bioinformatics 07-08-2013, 06:59 AM
Replies: 27
Views: 6,061
Posted By alittleboy
Hi @dpryan: Thank you for the update -- I...

Hi @dpryan:

Thank you for the update -- I also feel that ~1/2 not aligning to annotated genes is quite high... but unfortunately I don't know why.

The information above is from a single lane....
Forum: Bioinformatics 07-07-2013, 11:11 AM
Replies: 74
Views: 33,680
Posted By alittleboy
Hi @krespim: I had a question on MISO and...

Hi @krespim:

I had a question on MISO and posted here (http://seqanswers.com/forums/showthread.php?t=31723). Can you help me with that? Thanks! ;-)
Forum: Bioinformatics 07-07-2013, 11:09 AM
Replies: 2
Views: 2,577
Posted By alittleboy
Error: tagBam call failed when running pe_utils.py --compute-insert-len

Dear All:

I am using MISO to test for differential exon usage between a control and a treatment group. I got an error when computing the insert length distribution using pe_utils.py...
Forum: Bioinformatics 07-06-2013, 11:06 AM
Replies: 1
Views: 1,300
Posted By alittleboy
Smile Anyone familiar with this situation with MISO?...

Anyone familiar with this situation with MISO? Please share your thoughts. I really appreciate ;-)
Forum: Bioinformatics 07-02-2013, 12:00 PM
Replies: 0
Views: 1,249
Posted By alittleboy
DEXSeq questions on power and counting bins

I originally post this in the Bioconductor mailing list, but I hope that more colleagues can see it and help me clarify the questions. If you've seen this in the mailing list, please ignore this one ...
Forum: Bioinformatics 07-02-2013, 04:49 AM
Replies: 27
Views: 6,061
Posted By alittleboy
Hi @dpryan: Thanks for the clarifications!...

Hi @dpryan:

Thanks for the clarifications! Here is some summary statistics from the folder (that contains accepted_hits.bam, junctions.bed files, etc.) with the file name "left_kept_reads.info":
...
Forum: Bioinformatics 07-01-2013, 11:57 AM
Replies: 27
Views: 6,061
Posted By alittleboy
Hi Alejandro: Thanks for the update -- sorry...

Hi Alejandro:

Thanks for the update -- sorry I am a little confused by the different inputs from you, @krespim and the pasilla vignette... I apologize for my confusion. Here I list the steps that...
Forum: Bioinformatics 07-01-2013, 09:03 AM
Replies: 27
Views: 6,061
Posted By alittleboy
Yes, this time I used "-n" option when doing...

Yes, this time I used "-n" option when doing samtools sort, and got the merged_sort.bam file. However, when I continue to run:

samtools index merged_sorted.bam merged_sorted.bam.bai

It has the...
Forum: Bioinformatics 07-01-2013, 07:54 AM
Replies: 11
Views: 4,443
Posted By alittleboy
Hi @areyes: That's very clear! Thanks for...

Hi @areyes:

That's very clear! Thanks for the examples -- I see how important to understand it is the exonic region (exon bin) instead of real exon that constitutes the building block for DEXSeq...
Forum: Bioinformatics 07-01-2013, 07:41 AM
Replies: 0
Views: 666
Posted By alittleboy
Question What's the consequence of using only one lane

Hi All,

I am currently analyzing an RNA-Seq experiment which consists of two conditions, control and treatment. Each condition has 3 biological replicates. For each bio. reps., the samples are...
Forum: Bioinformatics 07-01-2013, 06:39 AM
Replies: 27
Views: 6,061
Posted By alittleboy
Hi @krespim: Thank you so much for the...

Hi @krespim:

Thank you so much for the instructions and suggestions! I've order the book you mentioned, and plan to read it carefully ;-)

I tried to use your correct approach for sorting the...
Showing results 1 to 25 of 60

 


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