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Forum: RNA Sequencing 12-02-2013, 08:13 AM
Replies: 0
Views: 1,324
Posted By neetu
Need help to get a DEseq or EdgeR example file

Hi,
I am a novice in RNA-seq data analysis.

I need a list of DEG from RNA-seq data. I need to test this list against some new workflows developed inhouse. Can anyone suggest how i can get such a...
Forum: Bioinformatics 06-17-2012, 09:51 PM
Replies: 0
Views: 1,477
Posted By neetu
Agilent Probe IDS

Hi,

We are developing a tool to analyze microarray data. For Affymetrix probe ids i have got the relevant page to hyperlink all the probes which the user input.
Can anyone suggest me to which...
Forum: Bioinformatics 02-06-2012, 09:20 PM
Replies: 0
Views: 1,646
Posted By neetu
warning message on running MACS

i am getting a warning message while running MACS
"WARN - Treatment tags and Control tags are uneven! FDR may be wrong!"

why am i getting this message, and what changes should i make in the...
Forum: Bioinformatics 01-12-2012, 03:09 AM
Replies: 0
Views: 1,767
Posted By neetu
how to export a Transfac matrix

I want to upload a matrix in .dat format in my inhouse tool for testing purpose. Transfac have matrices but i really don't know how to export them.
URL for the matrix needed to export is: ...
Forum: Bioinformatics 11-24-2011, 03:17 AM
Replies: 1
Views: 3,205
Posted By neetu
MACS version 1.3.0 versus MACS version 1.4.0

i have tried calling peaks by both the versions of MACS. incidentally i got a model with 1.3.7 but did not get any model with 1.4.0 a warning instead
(too few paired peaks (0) so I can not build...
Forum: Bioinformatics 10-18-2011, 03:50 AM
Replies: 1
Views: 2,825
Posted By neetu
FTP upload in galaxy

i tried uploading a data in galaxy via FTP method. the URL used is

ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE27619/GSE27619%5FRAW%2Etar

i get an error message as :Unable to...
Forum: Bioinformatics 10-17-2011, 03:23 AM
Replies: 1
Views: 2,069
Posted By neetu
Indel analysis from galaxy

there is a feature in galaxy http://main.g2.bx.psu.edu/
termed as NGS:indel analysis which have subtabs as Filter indels for SAM, extract indels from SAM...

can anyone please tell me what is the...
Forum: Bioinformatics 10-14-2011, 03:15 AM
Replies: 8
Views: 15,172
Posted By neetu
thanks a ton for your reply dpryan and peter....

thanks a ton for your reply dpryan and peter. your links are really helpful. one more doubt now arises is that is there a way by which we can get prealigned files. i till now presumed that we get...
Forum: Bioinformatics 10-13-2011, 03:19 AM
Replies: 8
Views: 15,172
Posted By neetu
i am actually having a problem, i opened this...

i am actually having a problem, i opened this page from GEO
http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE20116
this is an RNA-seq analysis for sure, if i need the data and i scroll...
Forum: Bioinformatics 10-13-2011, 01:44 AM
Replies: 8
Views: 15,172
Posted By neetu
Thanks a lot for your reply..i will try...

Thanks a lot for your reply..i will try searching..
Forum: Bioinformatics 10-12-2011, 10:00 PM
Replies: 8
Views: 15,172
Posted By neetu
RNA-seq analysis raw data format

Hello,

I am relatively new to this sequencing field. can anybody guide me with the basics and tell me what is the RNA-seq analysis raw data format. Is it .bed files or fastq files. How to find out...
Showing results 1 to 11 of 11

 


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