SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 56
Search took 0.00 seconds.
Search: Posts Made By: IBseq
Forum: Bioinformatics 11-30-2017, 09:14 AM
Replies: 1
Views: 2,073
Posted By IBseq
hi did you get an answer? ib

hi
did you get an answer?

ib
Forum: Bioinformatics 01-22-2014, 12:02 AM
Replies: 13
Views: 2,851
Posted By IBseq
vfs running

hi everyone
(if anyone is there!!!)

I run the vfs example 1.VFS.sys.check.pl and got nothing. this is the report after i submitted the job:

Make sure BWA is installed and is available in PATH...
Forum: Bioinformatics 01-21-2014, 02:32 AM
Replies: 13
Views: 2,851
Posted By IBseq
I meant different as it contains different lines....

I meant different as it contains different lines. Not sure if this is specific with the hbv4 genome (which i dont know much about!)
Forum: Bioinformatics 01-21-2014, 02:31 AM
Replies: 13
Views: 2,851
Posted By IBseq
Hello everyone, quick question about vfs: to...

Hello everyone,
quick question about vfs: to save my viral genome of interest, is is enough to use the fasta file from NCBI website (http://www.ncbi.nlm.nih.gov/nuccore/4927719?report=fasta) and...
Forum: Bioinformatics 01-16-2014, 11:16 PM
Replies: 13
Views: 2,851
Posted By IBseq
Thanks Marco, I have run 1.VFS.sys.check.pl...

Thanks Marco,
I have run 1.VFS.sys.check.pl but where can I see the output?
No error came up, so shall I assume everything is correctly installed with correct dependencies?

Thanks very much, ...
Forum: Bioinformatics 01-16-2014, 07:09 AM
Replies: 13
Views: 2,851
Posted By IBseq
hi everyone, hope I'm in the right place! ...

hi everyone,
hope I'm in the right place!

I need to use vfs to detect fusions in my sequenced samples.

I am a very beginner on unix, thus im havng problems to get started:
I have downloaded...
Forum: RNA Sequencing 12-02-2013, 03:57 PM
Replies: 6
Views: 2,935
Posted By IBseq
Hi Daniel77, did you get any answer on q1 and...

Hi Daniel77,
did you get any answer on q1 and q2?
I am also running cuffdiff without replicates and would like to understand how it does this

thanks
ibseq
Forum: Bioinformatics 11-15-2013, 11:28 AM
Replies: 5
Views: 3,980
Posted By IBseq
Hello guys, if anyone knows, could you please...

Hello guys,
if anyone knows, could you please tell me why is this happening:

i ran cufflinks on galaxy with default parameters and had satisfactory results.
I then ran the same samples with...
Forum: Bioinformatics 10-30-2013, 12:19 AM
Replies: 5
Views: 4,224
Posted By IBseq
hi all, can anyone tell em how to fix this? ...

hi all,
can anyone tell em how to fix this?

head(features(myGene))
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "features", for signature...
Forum: RNA Sequencing 10-24-2013, 04:37 AM
Replies: 61
Views: 33,458
Posted By IBseq
dear cummerbund users, i am trying to run the...

dear cummerbund users,
i am trying to run the following command:

library(cummeRbund)
cuff <- readCufflinks()
....

iso.diff <- diffData(isoforms(cuff))
iso.diff.top <-...
Forum: RNA Sequencing 10-18-2013, 12:28 AM
Replies: 61
Views: 33,458
Posted By IBseq
Dear all, any suggestion about this issue I...

Dear all,
any suggestion about this issue I have?

I run the following commands:
> library (cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required...
Forum: Bioinformatics 10-18-2013, 12:26 AM
Replies: 2
Views: 1,054
Posted By IBseq
Dear all, any suggestion about this issue I...

Dear all,
any suggestion about this issue I have?

I run the following commands:
> library (cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required...
Forum: Bioinformatics 10-16-2013, 02:04 AM
Replies: 15
Views: 15,718
Posted By IBseq
dear all, any suggestion more than wellcome! ...

dear all,
any suggestion more than wellcome!

<environment: namespace:cummeRbund>
> cuff<-readCufflinks(rebuild=T)
Creating database /home/bsib/Cuffdiff/caski/cuffData.db
Reading...
Forum: Bioinformatics 10-16-2013, 01:41 AM
Replies: 15
Views: 15,718
Posted By IBseq
im new to r btwa abd unix/linux as well... ...

im new to r btwa
abd unix/linux as well...

gosh!helpppp!
Forum: Bioinformatics 10-16-2013, 01:41 AM
Replies: 15
Views: 15,718
Posted By IBseq
Hi, I have human cervical samples. No...

Hi,
I have human cervical samples. No replicates. this one i posted is one of the samples I have compared with the negative sample...

i'm struggling writing down commands...! I need to create a...
Forum: Bioinformatics 10-15-2013, 06:12 AM
Replies: 15
Views: 15,718
Posted By IBseq
hi, can anyone help me out with this? >...

hi,
can anyone help me out with this?
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2...
Forum: Bioinformatics 10-18-2012, 01:50 AM
Replies: 16
Views: 11,852
Posted By IBseq
Hi Artur, yes, that makes sense. Thus I shall...

Hi Artur,
yes, that makes sense. Thus I shall not take in consideration the p/q values and their consequent significance.

I did follow the tophat/cufflinks/cuffcompare/cuffdiff pipeline, but I...
Forum: Bioinformatics 10-17-2012, 01:10 PM
Replies: 5
Views: 4,903
Posted By IBseq
hi robby, not sure if you sorted out but I write...

hi robby, not sure if you sorted out but I write it anyway...

"Maybe I do something wrong. I did the following:
1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
2. cuffdiff...
Forum: Bioinformatics 10-17-2012, 01:07 PM
Replies: 6
Views: 11,160
Posted By IBseq
hi all, i had the same prob and i was told to run...

hi all, i had the same prob and i was told to run cuffdiff WITHOUT the "N" option (perform quartile normalization)

hope it helps....
ib
Forum: Bioinformatics 10-17-2012, 01:03 PM
Replies: 3
Views: 20,818
Posted By IBseq
did you find a solution? I have the same...

did you find a solution? I have the same problem...

ib
Forum: Bioinformatics 10-17-2012, 01:02 PM
Replies: 3
Views: 20,818
Posted By IBseq
did you get any answer? ib

did you get any answer?

ib
Forum: Bioinformatics 10-17-2012, 01:00 PM
Replies: 16
Views: 11,852
Posted By IBseq
Calculating p-values from FPKM and more...

Hi Artur,
I read with interest your last conversation abt the statistic to be used.
I am new to this filed and very new to the statistic field, thus I am completely lost!

here my issue: I have...
Forum: Bioinformatics 10-17-2012, 05:17 AM
Replies: 17
Views: 11,315
Posted By IBseq
Hi mbblack, thanks. I think I understood your...

Hi mbblack,
thanks. I think I understood your point of view. I shall look at the data by simply looking at the fold change and ignoring the fpkm values equal to zero from both samples.

Thanks a...
Forum: Bioinformatics 10-17-2012, 02:20 AM
Replies: 17
Views: 11,315
Posted By IBseq
Hi, I was going through the cuffdiff manual...

Hi,
I was going through the cuffdiff manual where it says "If there are no replicates, the variance is measured across the conditions under the assumption that most transcripts are not...
Forum: Bioinformatics 10-16-2012, 08:57 AM
Replies: 17
Views: 11,315
Posted By IBseq
thanks mbblack, one thing i don't get...so you...

thanks mbblack,
one thing i don't get...so you suggest to rank by fpkm value, exclude those where this is=0 and then rank the rest by fold change? so this means that we do not consider whether they...
Showing results 1 to 25 of 56

 


All times are GMT -8. The time now is 01:29 PM.


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