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Forum: RNA Sequencing 07-23-2014, 07:40 PM
Replies: 35
Views: 25,491
Posted By choishingwan
Hi Tanya, From what I understand, the log2FC...

Hi Tanya,

From what I understand, the log2FC provided by the DESeq2 might be a bit different from that produced from the DESeq programme because it tried to perform a shrinkage according to the...
Forum: Bioinformatics 01-21-2014, 05:10 AM
Replies: 3
Views: 1,581
Posted By choishingwan
Thank you Michael, looking forward to the update

Thank you Michael, looking forward to the update
Forum: Bioinformatics 01-20-2014, 03:05 AM
Replies: 3
Views: 1,581
Posted By choishingwan
Problem with DESeq2 replaceOutliersWithTrimmedMean

Hi there,

I am currently using DESeq2 and have found some NA values in the p-values. From previous post, it was suggested that it is because of a 0 counts in all sample (therefore missing) and...
Forum: Bioinformatics 12-18-2013, 06:21 PM
Replies: 4
Views: 3,169
Posted By choishingwan
Try and see if those reads are all coming from...

Try and see if those reads are all coming from the same lane or if those are the second read of the read pair. Usually the lane will fail together or in general, the second read pair usually have a...
Forum: Bioinformatics 12-18-2013, 01:02 AM
Replies: 4
Views: 3,169
Posted By choishingwan
From my experience, RNA Sequencing reads does...

From my experience, RNA Sequencing reads does have a relatively high duplication rate base on its nature and most of the time I don't read into the duplication rate from the FastQC report and focus...
Forum: Bioinformatics 10-09-2013, 06:43 AM
Replies: 2
Views: 2,061
Posted By choishingwan
The simplest way might be to use awk? (but will...

The simplest way might be to use awk? (but will be slow)



something like that, I haven't tested the code though...
Forum: Bioinformatics 10-09-2013, 06:41 AM
Replies: 18
Views: 15,846
Posted By choishingwan
From my memory, you should be able to get a bam...

From my memory, you should be able to get a bam file from the TableRecalibration. From what I understand, you only have to merge samples (as in, really merge samples into one single bam file) when...
Forum: Bioinformatics 10-09-2013, 04:20 AM
Replies: 18
Views: 15,846
Posted By choishingwan
There's definitely no problem in using the latest...

There's definitely no problem in using the latest dbsnp file with the old gatk pipeline. As for the print read problem, I think that's when the version different take place. In my case, in the latest...
Forum: Bioinformatics 10-09-2013, 03:25 AM
Replies: 18
Views: 15,846
Posted By choishingwan
@vd4mindia: From your code, I guess you are...

@vd4mindia: From your code, I guess you are running GATK version before 2.6 right? You are right about using the dbsnp137. From the look of it it seems correct. In case if you want to use the latest...
Forum: Bioinformatics 10-09-2013, 03:08 AM
Replies: 15
Views: 7,785
Posted By choishingwan
I do have a set of data containing both Exome Seq...

I do have a set of data containing both Exome Seq and RNA Seq. It will be interesting to see how they correlate in terms of calling. Specifically, it will be interested to see how mark duplication...
Forum: Bioinformatics 10-09-2013, 02:50 AM
Replies: 18
Views: 15,846
Posted By choishingwan
I thought fixMate is no longer required by the...

I thought fixMate is no longer required by the GATK pipeline? And if you want to perform the fixMate then sortSam, you can run FixMate with the SO options in SortSam, then your output will be...
Forum: RNA Sequencing 07-28-2013, 11:22 PM
Replies: 35
Views: 25,491
Posted By choishingwan
Yes, that's true, those are the padj values

Yes, that's true, those are the padj values
Forum: RNA Sequencing 07-28-2013, 10:05 PM
Replies: 35
Views: 25,491
Posted By choishingwan
By turning off the cook's cutoff I was able to...

By turning off the cook's cutoff I was able to obtain a p-value for all the genes that have a p-value from DESeq and EdgeR but not from DESeq2. However, I also notice something interesting: Some of...
Forum: RNA Sequencing 07-25-2013, 03:18 AM
Replies: 35
Views: 25,491
Posted By choishingwan
I see, maybe I should try turning off the Cook's...

I see, maybe I should try turning off the Cook's filtering and see if these NA still persist.

Thank you
Forum: RNA Sequencing 07-24-2013, 08:13 PM
Replies: 35
Views: 25,491
Posted By choishingwan
Hi Michael, Thank you for your reply, my...

Hi Michael,

Thank you for your reply, my sessionInfo are as follow:


R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United...
Forum: RNA Sequencing 07-23-2013, 12:24 AM
Replies: 35
Views: 25,491
Posted By choishingwan
Hi there, in my case, I got some genes that were...

Hi there, in my case, I got some genes that were significant (padj of 0.000000000495 in DESeq and also 2.06326E-15 in edgeR) but got NA in DESeq2. I am not sure what is the particular behaviour of NA...
Forum: Bioinformatics 09-25-2012, 10:30 PM
Replies: 5
Views: 3,235
Posted By choishingwan
So I have just finished the test using the...

So I have just finished the test using the following code:



With a 7.8GB input, if I use bam_fetch, on average I got the following time:
real 1m42.9934s
user 1m40.7904s
sys 0m1.9088s

And...
Forum: Bioinformatics 09-21-2012, 08:33 AM
Replies: 5
Views: 3,235
Posted By choishingwan
I see, I will try and see if by using the...

I see, I will try and see if by using the bam_fetch instead of the read by read reading and see if the speed improves. Will come back to you once I have got the time done
Forum: Bioinformatics 09-21-2012, 07:33 AM
Replies: 5
Views: 3,235
Posted By choishingwan
There are a few problems I noted with the...

There are a few problems I noted with the bam_fetch, the first one most notably is that the reads returned from the bam_fetch functions sometimes behave rather funny. There was a time when I got read...
Forum: Bioinformatics 09-20-2012, 09:28 PM
Replies: 5
Views: 3,235
Posted By choishingwan
Quickly Reading Through a Bam file using C++ programme

Hi, I am currently trying to write some programme that will transverse the whole bam file in a short period of time.

The standard samtools api works extreme fast if I use bam_fetch (I can read...
Forum: Bioinformatics 05-17-2012, 03:15 AM
Replies: 22
Views: 4,740
Posted By choishingwan
Bill, I guess you might be able to solve the...

Bill, I guess you might be able to solve the problem of Cytoscape not showing anything by increasing the allowed ram for the programme. You may do that by following the instruction on Cytoscape's...
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