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Forum: Bioinformatics 05-07-2018, 09:17 AM
Replies: 0
Views: 1,283
Posted By xrao
featureCounts does not recognize BWA XA tag?

Hello,

I am using featureCounts option -M. In the user guide, it says if it is specified, multi-mapping reads will be counted. The program uses the ‘NH’ tag to find multi-mapping reads. But I used...
Forum: RNA Sequencing 01-04-2016, 07:08 AM
Replies: 4
Views: 4,682
Posted By xrao
Thank you! But we meant mean values for each...

Thank you! But we meant mean values for each group/condition.
Forum: RNA Sequencing 12-31-2015, 07:08 AM
Replies: 4
Views: 4,682
Posted By xrao
Have you found the answer? I am also curious....

Have you found the answer? I am also curious. Thank you!
Forum: RNA Sequencing 12-23-2014, 10:39 AM
Replies: 4
Views: 2,261
Posted By xrao
Problem solved. It turns out to be the library...

Problem solved. It turns out to be the library issue in the linux system. The code should be fine. Thank you all and Merry Christmas!
Forum: RNA Sequencing 12-23-2014, 06:10 AM
Replies: 4
Views: 2,261
Posted By xrao
> dim(countdata) [1] 20587 69 >...

> dim(countdata)
[1] 20587 69
> dim(colData)
[1] 69 1

Thank you for your reply!
Forum: RNA Sequencing 12-22-2014, 05:35 PM
Replies: 4
Views: 2,261
Posted By xrao
DESeq2 DESeqDataSetFromMatrix problem

Dear experts,

I encountered a strange problem when using the DESeqDataSetFromMatrix command from DESeq2. I have set up the countData and colData in the required format the same as the sample data...
Forum: Bioinformatics 05-27-2014, 08:20 AM
Replies: 6
Views: 17,710
Posted By xrao
The RG means RGID, right? Thank you for...

The RG means RGID, right? Thank you for explaining the concept very clearly. I now have another situation, one lane with multiple samples.

Lane 1: case1-normal case1-tumor1 case1-tumor2...
Forum: Bioinformatics 05-23-2014, 11:39 AM
Replies: 6
Views: 17,710
Posted By xrao
I think you can use the picard...

I think you can use the picard AddOrReplaceReadGroups.jar to add RG to the merged bam file. The RG information are important for samples.
Forum: RNA Sequencing 03-28-2014, 02:22 PM
Replies: 22
Views: 10,185
Posted By xrao
Hi, Alejandro I have a similar situation....

Hi, Alejandro

I have a similar situation. One thing that I am a little worried is, when seperating the data into 2 (part 1 with H24 and control, and part 2 with H48 and control) and do whole...
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