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Forum: RNA Sequencing 11-14-2013, 08:21 AM
Replies: 5
Views: 1,954
Posted By FLYINGDOLPHIN
Hi, I grep the pathogen sequence from the...

Hi,

I grep the pathogen sequence from the fastq file.

All the matched seuqence is 50bp.

Before the space is the end of my pathogen transcript. Any nucleotides following it, I don't know what...
Forum: Bioinformatics 11-13-2013, 08:02 PM
Replies: 1
Views: 1,690
Posted By FLYINGDOLPHIN
Hello, I am trying to make an annotation...

Hello,

I am trying to make an annotation files for the transportable elements in drosophila, which is not included in the normal annotation file. Can you give me some detail instruction as to how...
Forum: Bioinformatics 11-13-2013, 07:56 PM
Replies: 2
Views: 1,130
Posted By FLYINGDOLPHIN
construct annotation files

Hi all,

I am interested in checking the non-coding rna(for example, transposons) expression levels.However, there is no annotation file (GTF for example). Does anyone know how to make the file in...
Forum: RNA Sequencing 11-13-2013, 02:32 PM
Replies: 5
Views: 1,954
Posted By FLYINGDOLPHIN
Hi Gringer, Thanks for the quick reply. I...

Hi Gringer,

Thanks for the quick reply. I got the data after they are removed off the index sequences. All the fragments that I get are of equal length. I just don't why there are still...
Forum: RNA Sequencing 11-13-2013, 12:47 PM
Replies: 5
Views: 1,954
Posted By FLYINGDOLPHIN
extra sequence following transcript in RNA-seq ?

Hi,

I did a dual-seq with pathogen and host. I found more nucleotides after the total mRNA transcript(as annotation) from the pathogen. For each sequence that mapped to the pathogen transcript in...
Forum: Bioinformatics 06-03-2013, 11:04 AM
Replies: 0
Views: 1,661
Posted By FLYINGDOLPHIN
htseq--SAM line does not contain at least 11 tab-delimited fields

Hi,

I plan to use htseq to count the sorted sam files for DEseq analysis. However, after a few line, it reports error.

Error occured in line 3030067 of file ....._2_sorted.sam.
Error: ('SAM...
Forum: Bioinformatics 05-30-2013, 09:57 AM
Replies: 123
Views: 50,697
Posted By FLYINGDOLPHIN
Hi, Does deseq development version better...

Hi,

Does deseq development version better than the release version? The manual that i found on Bioconductor seems to aim for the development version since the "normalize=True" does not work. I am...
Forum: Bioinformatics 05-30-2013, 03:29 AM
Replies: 123
Views: 50,697
Posted By FLYINGDOLPHIN
Thanks! Q

Thanks!
Q
Forum: Bioinformatics 05-29-2013, 06:58 PM
Replies: 1
Views: 892
Posted By FLYINGDOLPHIN
ht-seq count

Hi,

I am using htseq-count to count the reads before using DeSeq.

I am not sure whether I need to use the option -m nonempty or union.

Does this affect the result of Deseq analysis?
...
Forum: Bioinformatics 05-29-2013, 06:35 PM
Replies: 123
Views: 50,697
Posted By FLYINGDOLPHIN
oh, it is a R package from the core installation....

oh, it is a R package from the core installation.
R version 2.11.1, biocinstall version 2.6.10.

Thanks.
Q
Forum: Bioinformatics 05-29-2013, 06:27 PM
Replies: 123
Views: 50,697
Posted By FLYINGDOLPHIN
Hi, I'd love to install deseq2. But I have a...

Hi,

I'd love to install deseq2. But I have a problem in installing in.


> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using...
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