SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 39
Search took 0.00 seconds.
Search: Posts Made By: Mchicken
Forum: Bioinformatics 08-02-2017, 06:57 AM
Replies: 0
Views: 498
Posted By Mchicken
DESeq2 for DE analysis in developmental stages of tomato pollen

Hey guys,

I have the following scenario. We performed MACE experiments (like RNA-seq but you produce only one read per transcript) for three developmental stages of tomato pollen (3 biological...
Forum: Bioinformatics 05-09-2017, 11:56 PM
Replies: 674
Views: 167,129
Posted By Mchicken
Thanks a lot for your helpful replies. It is now...

Thanks a lot for your helpful replies. It is now working perfectly :). One more question to the "xstag". I see that if the gene is on the + strand, R2 maps on+ and R1 maps on -. If I use "xstag=ss" I...
Forum: Bioinformatics 05-09-2017, 05:59 AM
Replies: 674
Views: 167,129
Posted By Mchicken
Hi, I try to align paired-end reads of Pisum...

Hi,

I try to align paired-end reads of Pisum sativum (pea) to the genome of Arabidopsis thaliana, as there is no reference genome for pea. I first tried H̀SAT2 but had alignment rates of ~4%....
Forum: Bioinformatics 04-26-2016, 12:30 AM
Replies: 1
Views: 944
Posted By Mchicken
Is nobody having an idea about this? :/

Is nobody having an idea about this? :/
Forum: Bioinformatics 04-21-2016, 08:33 AM
Replies: 1
Views: 944
Posted By Mchicken
Preprocessing before k-means clustering of expression data

Hey guys,

I want to perform k-means clustering of expression data (already normalized). I have two conditions (CO and HS) and three developmental stages (S1,S2,S3). So in total six samples...
Forum: Bioinformatics 02-26-2016, 01:17 AM
Replies: 6
Views: 1,460
Posted By Mchicken
Anyone out there who can explain the lambda...

Anyone out there who can explain the lambda estimation in more detail (probably with an example) or knows a nice tutorial?
Forum: Bioinformatics 02-15-2016, 12:09 AM
Replies: 6
Views: 1,460
Posted By Mchicken
This is actually where I have a problem. I...

This is actually where I have a problem. I estimate lambda by the read counts of a gene (lambda = read count) and then I test the null-hypothesis that Condition A and B have the same lambda. So why...
Forum: Bioinformatics 02-14-2016, 10:16 PM
Replies: 6
Views: 1,460
Posted By Mchicken
First of all, thanks for your quick answer...

First of all, thanks for your quick answer dpryan.

But I still do not get where the lambda is coming from and what you mean by "group".
Forum: Bioinformatics 02-12-2016, 06:38 AM
Replies: 6
Views: 1,460
Posted By Mchicken
Statistical models for DE

Hey guys,

I have some problems understanding the need for statistical models when dealing with differential expression in RNA-Seq. Of course I already used tools like DESeq2 or NOISeq....
Forum: Bioinformatics 09-03-2015, 02:26 AM
Replies: 1
Views: 881
Posted By Mchicken
One possibility would be the Flux simulator,...

One possibility would be the Flux simulator, which is simulating RNA-Seq experiments. In the .pro file you can see the actual amount of transcripts in your transcriptome, the number of produced...
Forum: Bioinformatics 09-03-2015, 01:26 AM
Replies: 4
Views: 2,753
Posted By Mchicken
I would recommend HTSeq count...

I would recommend HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). With -t you can specify the feature type on which you count (e.g. intron or exon). By making two runs, one...
Forum: Bioinformatics 09-02-2015, 05:34 AM
Replies: 0
Views: 714
Posted By Mchicken
Batman ears in our read distributions

Hey guys,

like everyone else we are observing uneven/non-uniform coverage in our RNA-Seq experiments and I know that there are several things influencing this coverage issue like GC-bias or...
Forum: Bioinformatics 07-16-2015, 05:02 AM
Replies: 5
Views: 1,446
Posted By Mchicken
Okay now to summarize: In my case, indeed...

Okay now to summarize:

In my case, indeed the library-type is fr-secondstrand as the R1 (forward) read maps in 5' to 3' direction of the mRNA.

And the reason to call it fr-secondstrand is that...
Forum: Bioinformatics 07-15-2015, 09:27 PM
Replies: 5
Views: 1,446
Posted By Mchicken
First of all thanks for your advice. I already...

First of all thanks for your advice. I already read this way of library determination somewhere.
Nevertheless there should be a logical explanation anyway. The company, which sequenced our samples...
Forum: Bioinformatics 07-15-2015, 06:02 AM
Replies: 5
Views: 1,446
Posted By Mchicken
strand-specific libraries / firststrand /secondstrand

Hey,

I`m still very uncertain when dealing with strand specific RNA-Seq data. Especially when using TopHat2 and Cufflinks, as these make use of the strand-information via the library-types.

I...
Forum: Bioinformatics 07-06-2015, 08:44 AM
Replies: 0
Views: 671
Posted By Mchicken
geometric mean vs arithmetic mean

Hey,

I was thinking about this question quiet often but always forgot to ask it here:

DESeq is using the geometric mean during normalization. What is the benefit of the geometric mean in...
Forum: Bioinformatics 06-22-2015, 10:14 PM
Replies: 2
Views: 703
Posted By Mchicken
So what I see in the IGV-Browser is, that all the...

So what I see in the IGV-Browser is, that all the R1 reads map on the gene-strand (coding strand) and all the R2 reads map on the opposite strand.

So is this now firststrand or secondstrand?

I...
Forum: Bioinformatics 06-22-2015, 09:05 AM
Replies: 2
Views: 703
Posted By Mchicken
Cufflinks XS tag

Hey guys,

I have an issue with my Sam files I want to use as input for Cufflinks. Unfortunately I trucated the lines of my Sam file right after the 11th column (due to disk space) and by this...
Forum: Bioinformatics 04-28-2015, 01:36 AM
Replies: 0
Views: 836
Posted By Mchicken
Wrong number of mapped reads in TopHat2 output

Hey guys,

I ran TopHat2 for paired-end data with "-g 1", so if there are multiple alignments with the same score, only one of these is reported randomly.

Here my TopHat2 output...
Forum: Bioinformatics 03-05-2015, 05:55 AM
Replies: 4
Views: 863
Posted By Mchicken
That is a common problem of TopHat2 that I also...

That is a common problem of TopHat2 that I also observed two months ago. It is also a problem for some of the piccard-tools which you might run on your SAM files.

Although the bitflag of paired...
Forum: Bioinformatics 01-29-2015, 03:26 AM
Replies: 6
Views: 1,971
Posted By Mchicken
To the last issue: According to...

To the last issue:

According to http://broadinstitute.github.io/picard/explain-flags.html a hook at the second position ("read mapped in proper pair") is what I was looking for. And here also the...
Forum: Bioinformatics 01-28-2015, 11:11 PM
Replies: 6
Views: 1,971
Posted By Mchicken
Thanks for your response Brian. This was indeed...

Thanks for your response Brian. This was indeed the reason for the concordant alignment with 100kbp distance.

But I still have the problem with the 177 bitflag, which tells me that the mate was...
Forum: Bioinformatics 01-28-2015, 06:36 AM
Replies: 6
Views: 1,971
Posted By Mchicken
Hey everybody, has this problem been solved?...

Hey everybody,

has this problem been solved?

I am running TopHat2 version 2.0.13 and use default options with --mate-inner-dist 50 and --mate-std-dev 20.

When I draw 2x 100bp with a distance...
Forum: Bioinformatics 09-09-2014, 04:44 AM
Replies: 3
Views: 881
Posted By Mchicken
It`s a strand specific and polyA-purified library...

It`s a strand specific and polyA-purified library with 150bp long paired-end reads. So we should have only mRNAs.
Forum: Bioinformatics 09-09-2014, 01:18 AM
Replies: 3
Views: 881
Posted By Mchicken
different duplication levels in forward reverse libraries

Hi guys,
we are currently analyzing RNA-seq libraries from tomato and used FastQC for this. Remarkably, comparing the duplication levels from the forward and reverse library of the same experiment...
Showing results 1 to 25 of 39

 


All times are GMT -8. The time now is 12:15 PM.


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