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Forum: Bioinformatics 05-28-2013, 12:02 AM
Replies: 313
Views: 107,187
Posted By honey
question about GTF file annotation in seqmonk

I am uploading a GTF file for annotation downloaded from Encode/ Broad but when I put search term as have been mentioned in Simon's post I dont find any of search term how I would add as custom...
Forum: Bioinformatics 04-17-2013, 12:51 PM
Replies: 1
Views: 1,251
Posted By honey
Bacteria intergenic regions RNA-seq

If I am specifically interested in differential expression of intergenic regions in bacterial RNA-seq. Do I need to have riodepleted/ ribo zero libraries or polA should work fine?

Thanks
Forum: Sample Prep / Library Generation 04-11-2013, 05:30 AM
Replies: 5
Views: 2,747
Posted By honey
noncoding RNA

I have a very basic question is there a rule what may be good for detection of noncoding RNA (long), -PE or SE longer read in case of ribo-depleted. Is there an advantage/ disadvantage of one over...
Forum: Bioinformatics 03-25-2013, 01:38 PM
Replies: 313
Views: 107,187
Posted By honey
Txt file import in seqmonk

I sit possible to bring rpkm values calculated outside seqmonk and import in as txt file. Will it allow me to use the downstream analysis steps like clustering etc. or not. Another question I have if...
Forum: Bioinformatics 01-15-2013, 10:02 PM
Replies: 0
Views: 1,017
Posted By honey
denovo assembly analysis after contigs generation

I am relatively new in denovo assembly research. I started with 2X100 Illumina data and have used Valvet to generated contigs for identification of bacterial genome. I have ref genome. The idea is to...
Forum: Bioinformatics 01-04-2013, 12:11 PM
Replies: 313
Views: 107,187
Posted By honey
Hi Simon, Great job! One suggestion if you...

Hi Simon,

Great job! One suggestion if you can add demo to plot density graphs across TSS or more precisely, how one can plot density graph across TSS as discussed in...
Forum: Bioinformatics 12-20-2012, 03:44 AM
Replies: 3
Views: 1,271
Posted By honey
extracting viral seq

Thanks that was helpful !!!
Forum: Bioinformatics 12-18-2012, 11:49 PM
Replies: 3
Views: 1,271
Posted By honey
extracting seq from viral genome

I have coordinates of a viral genome and would like to extract seq from viral genome. Is there a tool or easy way to upload the txt file of ordinates and it will give me seq (equal to what do in...
Forum: Bioinformatics 12-14-2012, 04:00 AM
Replies: 3
Views: 1,308
Posted By honey
Viral RNA-seq

Thanks syfo,

It is human virus and I have already checked human genes, no I am concerned with only viral genes expression.

Honey
Forum: Bioinformatics 12-13-2012, 10:38 AM
Replies: 3
Views: 1,308
Posted By honey
viral RNA-seq

I have a data for viral RNA-seq and wonder if Bowtie should be fine. Idealy we would use ToPhat but I guess it may not work in virus as there are all exons.

Thanks for sharing the info
Forum: Bioinformatics 11-27-2012, 05:00 AM
Replies: 1
Views: 1,099
Posted By honey
peak calling for virus chipseq

I am interested in identifying viral particles in a chipseq experiment ran on Hi-seq. I used viral antibody using to perform IP. Is there any special tool for calling peaks in such small genome as...
Forum: Bioinformatics 11-24-2012, 06:30 AM
Replies: 2
Views: 2,165
Posted By honey
wheter combine FASTq or bam files after alignment

I have some Hi-seq data from three samples. The underlying principal of experiment is there is an infection of bacteria and I am intrested in studying DE of human as well as bacterial genes. I have...
Forum: Bioinformatics 11-22-2012, 02:20 PM
Replies: 2
Views: 1,331
Posted By honey
comparision of edgR and DEseq

I would like to bring to attention the paper by yendrek et al 2012
http://www.ncbi.nlm.nih.gov/pubmed/22980220
where they have pointed out some limitations of each method for RNA-seq analysis. It...
Forum: Bioinformatics 11-05-2012, 02:55 AM
Replies: 1
Views: 1,056
Posted By honey
instalation of breakdancer

I see lot of papers on usage of breakdancer, no one from this forum is ready to help me out pl

Thanks:(
Forum: Bioinformatics 11-03-2012, 07:04 PM
Replies: 1
Views: 1,056
Posted By honey
breakdancer instalation

Folks I have very baisc problem with Breakdancer instalation. My working server is x86_64 centos 6. I downlaoded the package from http://sourceforge.net/projects/breakdancer/files/
however I dont...
Forum: Bioinformatics 10-21-2012, 11:08 PM
Replies: 0
Views: 914
Posted By honey
TopHat multi hits

In addition to reporting the best (or primary) alignments (the original TopHat behavior), TopHat 2 can report the secondary alignments up to 20 (the default) paired or single alignments (see...
Forum: Bioinformatics 10-21-2012, 07:21 PM
Replies: 7
Views: 2,849
Posted By honey
What software

Which software are you using - commercial?
Honey
Forum: Bioinformatics 10-15-2012, 04:53 PM
Replies: 6
Views: 2,561
Posted By honey
RNA-seq

billstevens,
Dont give up. Take it as a learning step. I dont know much of your labs focus however, I believe Confirm a bunch of genes by RT PCR, then show with few immunofluoresence/ western or...
Forum: Bioinformatics 10-15-2012, 04:47 PM
Replies: 313
Views: 107,187
Posted By honey
Custom genome in seqmonk

I have a bacterial genome and is well documented at NCBI meaning has Fasta file as well annotation. However the particular organism is not there in seqmonk. Can I use custom annotation for my...
Forum: Bioinformatics 10-07-2012, 09:01 PM
Replies: 3
Views: 1,393
Posted By honey
annotation for viral genome

It has NCBI accession number.
Forum: Bioinformatics 10-02-2012, 09:37 AM
Replies: 3
Views: 1,393
Posted By honey
annotation for viral genome

I am working on chipseq data for virus and wonder is there a tool to annotate the genome. I have FAStq file as well as NCBI accession no which will have all annottaions. Doing mannual may add errors...
Forum: Bioinformatics 09-02-2012, 01:38 PM
Replies: 0
Views: 785
Posted By honey
question about use of Mev to generate a fig.

I found a paper @ http://genome.cshlp.org/content/21/8/1313.full#fn-1
and have a question about Fig 3B it is mentioned that the said fig from Chip-seq data was created using Mev tools /TM4 tools...
Forum: Bioinformatics 08-20-2012, 08:48 PM
Replies: 5
Views: 2,121
Posted By honey
Cool Single cell RNA-seq

I use Galaxy a lot, Could you please specify which tool you are referring to for Single cell RNA-seq. Am I missing something?
Forum: Bioinformatics 08-20-2012, 04:49 AM
Replies: 5
Views: 2,121
Posted By honey
single cell RNA seq

Any suggestion or experience to share on this?
Forum: Bioinformatics 08-16-2012, 07:42 PM
Replies: 5
Views: 2,121
Posted By honey
Single cell RNAseq _ Transcriptome sequence

I have data which has ben generated from Single cells (Stem cells/ cancer cells), I was wondering if some one has work flow for such anlaysis or any open source tools if some one has tested the tool....
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