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Forum: Bioinformatics 02-16-2017, 09:19 AM
Replies: 20
Views: 9,857
Posted By Gonza
glad it worked!

glad it worked!
Forum: Bioinformatics 02-15-2017, 05:24 AM
Replies: 20
Views: 9,857
Posted By Gonza
Hi, This is what i was getting. ...

Hi,

This is what i was getting.



[Fri Jan 6 12:35:41 2017] Beginning transcriptome assembly merge

-------------------------------------------
Forum: Bioinformatics 02-08-2017, 11:41 AM
Replies: 20
Views: 9,857
Posted By Gonza
Cufflinks duplicated genes error

Hi all,

I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was...
Forum: Bioinformatics 07-07-2016, 05:03 AM
Replies: 2
Views: 1,223
Posted By Gonza
Thanks Richard. I had seen that, but it is...

Thanks Richard.
I had seen that, but it is still confusing. In my experience, when you submit biological replicates to GEO each biorep gets its own SRA. Should I analyze these as bioreplciates?
...
Forum: Bioinformatics 07-06-2016, 01:19 PM
Replies: 2
Views: 1,223
Posted By Gonza
Single sample, more than one SRA file

Hello All,

I want to download some samples from the SRA (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22411) but sometimes a single sample has more than one SRA file, which is a bit...
Forum: RNA Sequencing 06-29-2016, 03:22 PM
Replies: 3
Views: 2,408
Posted By Gonza
Hi All, I will be soon mapping repetitive...

Hi All,

I will be soon mapping repetitive sequence and I have a couple of questions. It is my understanding that it is error-prone to map repetitive sequences. Is this something that tophat2 can...
Forum: Bioinformatics 02-01-2016, 01:08 AM
Replies: 6
Views: 3,887
Posted By Gonza
thanks, will look into Qualimap

thanks, will look into Qualimap
Forum: Bioinformatics 01-31-2016, 12:51 PM
Replies: 6
Views: 3,887
Posted By Gonza
Hi GenoMax I am mapping Illumina reads to a...

Hi GenoMax

I am mapping Illumina reads to a indexed genome with soap Version: 2.21 http://soap.genomics.org.cn/soapaligner.html

It seems to work fine, the only problem is that i cannot find the...
Forum: Bioinformatics 11-02-2015, 08:55 AM
Replies: 6
Views: 3,887
Posted By Gonza
Chip-seq mappers

Hello Geno Max and all,

I am inquiring about Chip-seq mapping software. I am using the Arabidopsis TAIR10 genome as a reference.

I have used for RNA-seq tophat2 to account for splicing, which...
Forum: Bioinformatics 08-21-2015, 02:17 PM
Replies: 20
Views: 9,857
Posted By Gonza
Hello All, I am having the same problem....

Hello All,

I am having the same problem. Thanks for the help



[Fri Aug 21 18:11:42 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Fri Aug 21...
Forum: Bioinformatics 06-09-2015, 05:38 PM
Replies: 9
Views: 6,360
Posted By Gonza
Hi all, I am trying to figure out how to...

Hi all,
I am trying to figure out how to compare arrays vs RNAseq. I am not really familiar with arrays, but I am a little bit concerned that we compare 'apples with pears'. I think RNA-seq and...
Forum: RNA Sequencing 04-18-2015, 09:48 AM
Replies: 4
Views: 1,637
Posted By Gonza
Hi, I did run htseq-count with default parameters...

Hi, I did run htseq-count with default parameters and worked well for downstream analysis. Now, there is one thing I'd like to do which is know how many reads aligned to to exons, UTRs and other...
Forum: RNA Sequencing 04-12-2015, 10:06 AM
Replies: 19
Views: 4,287
Posted By Gonza
thanks, appreciate the feedback. Two more things...

thanks, appreciate the feedback. Two more things ....

* this problematic libraries has 4 million reads less than the others. Will cufflinks account for these differences too?

* should i keep...
Forum: RNA Sequencing 04-12-2015, 06:49 AM
Replies: 19
Views: 4,287
Posted By Gonza
i guess, on the positive side, is better to have...

i guess, on the positive side, is better to have an 'exotic' contamination rather than the usual e.coli :):)

Would you suggest dumping these 2 libraries? As i mentioned, I still map 8MR to the...
Forum: RNA Sequencing 04-12-2015, 06:18 AM
Replies: 19
Views: 4,287
Posted By Gonza
the facility made and sequence them. They were...

the facility made and sequence them. They were multiplexed and pooled in a single lane.
I have not look at the barcode in the contaminated reads, i guess that is a good idea (Those barcode should...
Forum: RNA Sequencing 04-12-2015, 05:01 AM
Replies: 19
Views: 4,287
Posted By Gonza
Thanks Brian. Here are the details. Same...

Thanks Brian. Here are the details. Same question, will this affect downstream analysis (I ask because I have ~8 MR mapped to my reference genome) ?

--

1) Mapping to TAIR10. Illumina HiSeq2500...
Forum: RNA Sequencing 04-10-2015, 05:51 PM
Replies: 19
Views: 4,287
Posted By Gonza
GenoMax, I am glad to see you in this Forum, I'd...

GenoMax, I am glad to see you in this Forum, I'd like to get your opinion.

2 out of 15 of my libraries have low mapping rates (~60%) when using tophat. The rest are good (~94%). The 60% of these...
Forum: Bioinformatics 04-10-2015, 05:38 PM
Replies: 5
Views: 3,318
Posted By Gonza
Hi, I have a quick follow up...

Hi,

I have a quick follow up question......I am using that perl script to see why i am getting sooo low % of mapped reads (60%). When i run it i only pull ~ 11 samples of ~ 120 bp (not really a...
Forum: RNA Sequencing 04-02-2015, 10:35 AM
Replies: 22
Views: 26,514
Posted By Gonza
Thanks Blakeoft, will look into that ! G

Thanks Blakeoft, will look into that !
G
Forum: RNA Sequencing 04-02-2015, 09:05 AM
Replies: 22
Views: 26,514
Posted By Gonza
Hi Blakeoft I have used the suggestion you...

Hi Blakeoft

I have used the suggestion you provided a while ago to get the names of the genes (not only XLOC) when using cummeRbund. I am now wondering if there is there a way to get the genes ID...
Forum: Bioinformatics 01-29-2015, 07:26 AM
Replies: 123
Views: 46,909
Posted By Gonza
Hi all, I am new to DEseq2. Maybe this is...

Hi all,

I am new to DEseq2. Maybe this is silly question, but I do not understand why meanSdPlot fails.... any ideas to solve this problem?


library("vsn")
par(mfrow=c(1,3))
notAllZero <-...
Forum: Bioinformatics 12-20-2014, 12:25 PM
Replies: 3
Views: 2,983
Posted By Gonza
Hello Adrian, I am struggling with this too, does...

Hello Adrian, I am struggling with this too, does that mean you have to have the gtf file and the genome? Do you use genome.fa ? genome after you run bowtie-build?

Thanks
Forum: Bioinformatics 12-20-2014, 11:42 AM
Replies: 14
Views: 9,417
Posted By Gonza
Thank for your reply. I am still struggling with...

Thank for your reply. I am still struggling with this. I have included the gtf filed i used in cufflinks/cuffdiff but I still get the same error.

Any ideas?
Thanks again

rm(list=ls())...
Forum: Bioinformatics 12-17-2014, 10:54 AM
Replies: 36
Views: 18,336
Posted By Gonza
Hi all, I manually removed rRNA using the...

Hi all,

I manually removed rRNA using the Linux command:

$ grep -v 'rRNA' genes.gtf > new_genes.gtf

One question though, if you are looking for gene differential expression between...
Forum: Illumina/Solexa 12-04-2014, 09:03 AM
Replies: 1
Views: 1,301
Posted By Gonza
Hi, You can get standard desalted primers...

Hi,

You can get standard desalted primers and have the same results as if you'd order HPLC purified ones. This will help:
...
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