SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 51
Search took 0.02 seconds.
Search: Posts Made By: rozitaa
Forum: Bioinformatics 03-31-2015, 03:58 AM
Replies: 39
Views: 11,066
Posted By rozitaa
Thanks a lot Micheal!

Thanks a lot Micheal!
Forum: Bioinformatics 03-30-2015, 07:04 AM
Replies: 39
Views: 11,066
Posted By rozitaa
I see!! I cannot wait till April 17th since I...

I see!! I cannot wait till April 17th since I have deadline. And it is hard for me to install the developmental version of R! Is there any other solution for my problem?
Forum: Bioinformatics 03-30-2015, 06:51 AM
Replies: 39
Views: 11,066
Posted By rozitaa
Thanks a lot Micheal! I got the idea! The...

Thanks a lot Micheal! I got the idea!

The only problem that I have now is I am using HTSeq-count data this my code:
design <- ~ gut_microbiota + gut_microbiota:animal.nested +...
Forum: Bioinformatics 03-30-2015, 04:38 AM
Replies: 39
Views: 11,066
Posted By rozitaa
Hi Michael, I have also kinda same...

Hi Michael,

I have also kinda same experimental design and I tried to use your suggestions in this thread but still I get the same error regarding to linear combination.
In my project each sample...
Forum: Bioinformatics 03-26-2015, 11:13 AM
Replies: 123
Views: 44,893
Posted By rozitaa
I ran a code like this (hope it is the correct...

I ran a code like this (hope it is the correct one?!):

dds_LRT_liver <- nbinomLRT(dds[, dds$tissue=='liver'], full=~gut_microbiota, reduced=~1)
dds_LRT_PC <- nbinomLRT(dds[, dds$tissue=='PC'],...
Forum: Bioinformatics 03-26-2015, 10:57 AM
Replies: 123
Views: 44,893
Posted By rozitaa
Hi, I have recently have changed from DESeq...

Hi,

I have recently have changed from DESeq to DESeq2. So I need some help in designing my contrast for the binomial tests. This is my design table:

sample tissue gut_microbiota
1 5231 Si5 GF...
Forum: Bioinformatics 03-26-2015, 08:00 AM
Replies: 9
Views: 10,371
Posted By rozitaa
Thanks! So I will remove muss_log!

Thanks!
So I will remove muss_log!
Forum: Bioinformatics 03-26-2015, 06:38 AM
Replies: 9
Views: 10,371
Posted By rozitaa
How? I cannot understand that!!! It's true that...

How? I cannot understand that!!! It's true that each replicates can only have one gut_microbiota status but also for each sample I have three measurements (i.e. measuring three different tissues)...
Forum: Bioinformatics 03-26-2015, 06:16 AM
Replies: 9
Views: 10,371
Posted By rozitaa
dds =...

dds = DESeqDataSetFromHTSeqCount(sampleTable=sample_table, directory='~/dataAnalysis/Petia/barley_mice_rna-seq/htseq/', design= ~ muss_log + tissue + gut_microbiota)
Forum: Bioinformatics 03-26-2015, 05:28 AM
Replies: 9
Views: 10,371
Posted By rozitaa
Hi, I also get the same error but I don't...

Hi,

I also get the same error but I don't have same columns as N. has!!! Can anyone help me with this? mine look like this:

muss_log tissue gut_microbiota
1 5231 Si5 GF
2 5231 PC GF...
Forum: Bioinformatics 03-16-2015, 06:07 AM
Replies: 2
Views: 2,322
Posted By rozitaa
Thanks a lot! exactly that was the problem!

Thanks a lot! exactly that was the problem!
Forum: Bioinformatics 03-05-2015, 01:49 PM
Replies: 5
Views: 2,140
Posted By rozitaa
Hi Thanks for quick answer. I have worked with...

Hi Thanks for quick answer. I have worked with Qiime before. But I mean shotgun sequencing not 16s rRNA analysis!
Forum: Bioinformatics 03-05-2015, 01:21 PM
Replies: 5
Views: 2,140
Posted By rozitaa
Shotgun Metagenomics data analysis

Hi,

I am new to shotgun metagenomics analysis. I have a project on the human gut microbiota. I know about MG-rast but I want to analyze my data by my own. I have done the quality checking and...
Forum: Bioinformatics 02-26-2015, 06:00 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Thanks everyone! Now it is aligning perfectly...

Thanks everyone! Now it is aligning perfectly fine with TopHat! to sum up, I got the reads inner size from aligning firstly against transcriptomics reference by bowtie and then I aligned against...
Forum: Bioinformatics 02-26-2015, 12:24 AM
Replies: 21
Views: 5,279
Posted By rozitaa
I might have caught up the problem when I align...

I might have caught up the problem when I align it with only single end reads (readI). These are RNA-seq data that I am trying to map against genome reference. with bowtie I cannot get the splice...
Forum: Bioinformatics 02-26-2015, 12:19 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Oh no this is not the problem sorry for...

Oh no this is not the problem sorry for confusion. This is my fault in naming the files incorrectly in previous step! The R1_unpaired.fq is supposed to be named R2_paired.fq!!!
Forum: Bioinformatics 02-24-2015, 06:35 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Thanks Phillip! I think it should be like that...

Thanks Phillip! I think it should be like that since now that I am aligning only read one I can get approximately the whole aligned!!! Sure I will try to align it against a transcript reference.
Forum: Bioinformatics 02-24-2015, 06:32 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Thanks for nice explanation!

Thanks for nice explanation!
Forum: Bioinformatics 02-24-2015, 06:30 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Well it should be trimmed!!

Well it should be trimmed!!
Forum: Bioinformatics 02-24-2015, 05:26 AM
Replies: 21
Views: 5,279
Posted By rozitaa
I attached plots and statistical tables for two...

I attached plots and statistical tables for two different samples one from read one end and read two for the other sample! I don't have any idea what is the cutoff kmer enrichment. Can you please...
Forum: Bioinformatics 02-24-2015, 05:14 AM
Replies: 21
Views: 5,279
Posted By rozitaa
I am using version 2.0.6!!!

I am using version 2.0.6!!!
Forum: Bioinformatics 02-24-2015, 04:49 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Now I was also checking my sam file and...

Now I was also checking my sam file and interestingly some of my sam alignment lines don't have all sam fields! like this one:



Do you have any idea about this?
Forum: Bioinformatics 02-24-2015, 04:37 AM
Replies: 21
Views: 5,279
Posted By rozitaa
No I am aligning to the genome reference! Because...

No I am aligning to the genome reference! Because later on I want to align it by TopHat. So this is only a way to get idea about inner distance. But I can try star also.
I have had several...
Forum: Bioinformatics 02-24-2015, 04:17 AM
Replies: 21
Views: 5,279
Posted By rozitaa
Problem with the insert size of RNA-seq paired end reads!

The problem is that I cannot get a huge part of my RNA-seq data aligned!
These are some samples from the liver, intestine and colon of mice. We are analyzing the expression level of their genes. The...
Forum: Bioinformatics 02-17-2015, 11:52 PM
Replies: 2
Views: 2,322
Posted By rozitaa
clusterProfiler a tool for GSE analysis

Hi,

currently I am using clusterProfiler for gene set analysis and pathway analysis. but it seems some of the functions in the manual cannot be found in the R! such as gseGO(), getGeneSet() or...
Showing results 1 to 25 of 51

 


All times are GMT -8. The time now is 08:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO