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Forum: Bioinformatics 09-19-2019, 10:38 AM
Replies: 0
Views: 790
Posted By miaom
how to calculate DEG in a certain cluster using Seurat

I am a new user of Seurat, and I'd like to know how to correctly calculate the DEG from a certain cluster/sub-population?

Here are some basic description about the data I have and steps I use - ...
Forum: RNA Sequencing 01-10-2014, 10:21 PM
Replies: 2
Views: 5,470
Posted By miaom
thank :) You helped a looot!

thank :)
You helped a looot!
Forum: RNA Sequencing 01-10-2014, 06:51 PM
Replies: 2
Views: 5,470
Posted By miaom
Cufflink/Cuffdiff how to get fpkm for individual sample

I have 3 groups of samples (A, B and C), and n=4 for each group (12 in total)

Question 1.
Cuffdiff output only gives group-level averaged fpkm. If i want to run some correlation tests for the...
Forum: RNA Sequencing 12-10-2013, 10:03 PM
Replies: 4
Views: 4,677
Posted By miaom
edgeR: how to calculate group average/means ?

I am trying edgeR now to find deferentially expressed genes.
I have run
d <- DGEList(counts=data,group=g,lib.size=libSizes)
d <- calcNormFactors(d)
d <-...
Forum: RNA Sequencing 12-09-2013, 05:26 PM
Replies: 1
Views: 1,564
Posted By miaom
DEXSeq - condition / group level average

I am using DEXSeq to find deferentially expressed exons. But I wonder except for the statistics, is it possible to calculate the average/mean of the exon expressions in each condition/groups? If...
Forum: RNA Sequencing 12-01-2013, 10:24 PM
Replies: 3
Views: 2,328
Posted By miaom
I think the parameters (--mate-inner-dist,...

I think the parameters (--mate-inner-dist, --mate-std-dev) are for Tophat only. Bowtie does not need to specify them.
Running bowtie can generate SAM files, which contain information about fragment...
Forum: RNA Sequencing 12-01-2013, 12:25 PM
Replies: 0
Views: 1,278
Posted By miaom
Picard-tools or Trimmomatic flip read from FR or RF??

I have some PE RNAseq reads contaminated with adapter sequences.

Before removing the adapters, i mapped the reads using bowtie2 -> samtools -> picard-tools "CollectInsertSizeMetrics.jar" and got...
Forum: RNA Sequencing 12-01-2013, 12:06 PM
Replies: 3
Views: 2,328
Posted By miaom
How to set Tophat insert size

correctly setting 2 parameters in Tophat:
--mate-inner-dist
--mate-std-dev
should be very important, but i have no idea how to set them without running bowtie (or bowtie2) -> samtools -> picard...
Forum: RNA Sequencing 08-08-2013, 10:46 AM
Replies: 7
Views: 4,551
Posted By miaom
In the second reads, though I think there is...

In the second reads, though I think there is something not right, the YT:Z:<S> is "CP". Should it mean align discordantly or concordantly?
...
Forum: RNA Sequencing 08-08-2013, 10:27 AM
Replies: 7
Views: 4,551
Posted By miaom
your answers help a lot!!! Thank you so much!

your answers help a lot!!! Thank you so much!
Forum: RNA Sequencing 08-07-2013, 03:47 PM
Replies: 7
Views: 4,551
Posted By miaom
bowtie2 output, concordant vs. discordant reading??

Here are several lines from the sam file obtained from running bowtie2.
Could anybody tell me, how to tell if the mapping is concordant or discordant mapping?
Many thanks!!
...
Forum: RNA Sequencing 05-23-2013, 01:40 PM
Replies: 3
Views: 1,865
Posted By miaom
reason for low mapping rate??

we did RNASeq using HiSeq 2000 100PE. When the data were back, I mapping them to the reference sequence, but got very low mapping rate (30-40%). I asked around, some people suggest to checked for...
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