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Forum: Bioinformatics 09-25-2015, 02:40 PM
Replies: 5
Views: 3,797
Posted By stormin
Sorry to dig up the old post, I think my question...

Sorry to dig up the old post, I think my question is relevant to this discussion.

From practical point of view, technical replicates from the same RNA sample can be merged together into a single...
Forum: Bioinformatics 06-16-2015, 10:01 AM
Replies: 4
Views: 1,437
Posted By stormin
Sounds good, thanks!

Sounds good, thanks!
Forum: Bioinformatics 06-16-2015, 09:32 AM
Replies: 4
Views: 1,437
Posted By stormin
Thanks for the concise answer, are there any...

Thanks for the concise answer, are there any scripts that can do this conversion?
Forum: Bioinformatics 06-15-2015, 04:26 PM
Replies: 4
Views: 1,437
Posted By stormin
HTSeq count to expression level

Hi,

I understand that the raw HTSeq output is number of reads mapped to each gene (correct me if I'm wrong). Is there an easy way of converting counts to gene expression? The method should take...
Forum: Bioinformatics 05-07-2015, 11:07 AM
Replies: 9
Views: 1,529
Posted By stormin
Hi mbblack, I think expression level can be...

Hi mbblack, I think expression level can be correlated with function and particular proteins, due to their function, may have very low gene expression level and/or protein expression level because...
Forum: Bioinformatics 05-07-2015, 09:05 AM
Replies: 9
Views: 1,529
Posted By stormin
Thanks for all of the responses. To me, this...

Thanks for all of the responses. To me, this sounds like it's coming from personal experience of looking at multiple tissue specific profiles. I am wondering if any prior papers have delve into this...
Forum: Bioinformatics 05-06-2015, 08:52 PM
Replies: 9
Views: 1,529
Posted By stormin
Actually I mean if there are any prior research...

Actually I mean if there are any prior research in what types of protein/genes are typically low expressing. For example, we know housekeeping genes are typically always on and expressed in cell at...
Forum: Bioinformatics 05-06-2015, 11:23 AM
Replies: 9
Views: 1,529
Posted By stormin
What types of genes/protein are lost with low depth?

Methods for both determining differential expression of mRNA and protein expression levels depend on the depth of the sequencing/MS runs. Are there any previous studies that systematically looked at...
Forum: Bioinformatics 12-08-2014, 12:38 PM
Replies: 13
Views: 2,857
Posted By stormin
Thanks for all the inputs, looks like updating...

Thanks for all the inputs, looks like updating fixed this bug!
Forum: Bioinformatics 12-05-2014, 09:27 PM
Replies: 13
Views: 2,857
Posted By stormin
That shouldn't be a problem, there are more than...

That shouldn't be a problem, there are more than 700gb left on the hard-drive.
Forum: Bioinformatics 12-05-2014, 06:52 PM
Replies: 13
Views: 2,857
Posted By stormin
I think I installed samtools before tophat....

I think I installed samtools before tophat. Everything works actually with tophat and I am able to use the BAM files for HTSEQ and then DESEQ2.
Forum: Bioinformatics 12-05-2014, 05:24 PM
Replies: 13
Views: 2,857
Posted By stormin
Version number is 0.1.19-4428cd It...

Version number is 0.1.19-4428cd



It looks like no temporary files are created. The command throws the error message after less than a minute of running (actually I'm not sure how long it...
Forum: Bioinformatics 12-05-2014, 04:14 PM
Replies: 13
Views: 2,857
Posted By stormin
Nope, I would get the same error message.

Nope, I would get the same error message.
Forum: Bioinformatics 12-05-2014, 11:40 AM
Replies: 13
Views: 2,857
Posted By stormin
indexing tophat bam files

Hi,

I am having trouble using samtools to index my tophat output for IGV viewing. The tophat output bam should be sorted (although I am having trouble too using samtools to sort the tophat output...
Forum: Bioinformatics 10-21-2014, 02:22 PM
Replies: 4
Views: 1,121
Posted By stormin
Ahh, thanks for your help. Looks like excel...

Ahh, thanks for your help. Looks like excel indeed is to be blamed for this error. I just checked my dataset using python, looks all clear!
Forum: Bioinformatics 10-21-2014, 11:52 AM
Replies: 4
Views: 1,121
Posted By stormin
DESeq2 bizarre error - dates in gene list

Hey guys, I am running into a really weird problem in my RNA-seq analysis pipeline. In my final DESeq2 output, in the first column where the gene names are, there are a few entries that are purely...
Forum: RNA Sequencing 09-08-2014, 12:48 PM
Replies: 5
Views: 1,359
Posted By stormin
But there must be a lower limit on this question....

But there must be a lower limit on this question. For example, 15 minutes post treatment is probably not going to be enough time for new mRNA to accumulate. Now, what about a hour? I just want to see...
Forum: RNA Sequencing 09-08-2014, 11:56 AM
Replies: 5
Views: 1,359
Posted By stormin
earliest detectable RNAseq differential expression?

We are trying to determine the best time points to be used for detecting transient transcriptome response after treatment. Are there any studies done prior that looked at the best times for...
Forum: Bioinformatics 09-07-2014, 09:54 AM
Replies: 6
Views: 3,934
Posted By stormin
Hi Devon, so what I am trying to do is to use...

Hi Devon, so what I am trying to do is to use DESeq2 to compare two data manipulation methods. The same RNAseq fastq dataset was used in tophat. Condition1 used coverage search (which takes a lot...
Forum: Bioinformatics 09-06-2014, 01:31 PM
Replies: 6
Views: 3,934
Posted By stormin
Hmm, that didn't work unfortunately. Here is my R...

Hmm, that didn't work unfortunately. Here is my R script with the same error message. I'm new to R, so sorry in advance if there is a very obvious mistake. Thanks!




Same error message plus...
Forum: Bioinformatics 09-06-2014, 10:39 AM
Replies: 6
Views: 3,934
Posted By stormin
DESeq2 error

Hi all,

New to DESeq2 and getting error consistently while running this line:

dds <- DESeq(dds)

The error message:

estimating size factors
estimating dispersions
Forum: Bioinformatics 08-27-2014, 08:00 PM
Replies: 3
Views: 1,298
Posted By stormin
That make sense. Thanks!

That make sense. Thanks!
Forum: Bioinformatics 08-27-2014, 05:18 PM
Replies: 3
Views: 1,298
Posted By stormin
Illumina HiSeq2500 data

I am trying to determine the method used to generate my RNAseq data. On the Illumina website, the read length are either 1*36bp or 2*50bp. My fastq reads are non-strand-specific and non-paired...
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