SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 10 of 10
Search took 0.00 seconds.
Search: Posts Made By: edm1
Forum: RNA Sequencing 10-09-2014, 10:02 AM
Replies: 11
Views: 2,323
Posted By edm1
Hi, thanks for the reply. Within group variances...

Hi, thanks for the reply. Within group variances are very low. In mutants the (95%?) CI is 0-0.216 and wild type is 15.15-26.33. We would expect this to be highly significant.
Forum: RNA Sequencing 10-09-2014, 06:43 AM
Replies: 4
Views: 1,083
Posted By edm1
Is counts formatted correctly, does ...

Is counts formatted correctly, does
head(counts)
look like you'd expect?

Is there a reason you are not using DESeq2? In DESeq2 you'd use DESeqDataSetFromMatrix instead of newCountDataSet:

dds...
Forum: RNA Sequencing 10-09-2014, 03:17 AM
Replies: 11
Views: 2,323
Posted By edm1
Cuffdiff v2.2.1 differential expression test bug?

Hi,

Can anyone spot if I am doing something wrong. At the moment I am convinced there is a bug. In gene_exp.diff, my control gene (the one that is knocked out) is being reported as not...
Forum: Bioinformatics 06-18-2014, 03:43 AM
Replies: 5
Views: 10,798
Posted By edm1
I had this problem when I was using the latest...

I had this problem when I was using the latest version of Bowtie. Try downgrading to Bowtie2 v2.2.1.
Forum: Bioinformatics 06-17-2014, 04:51 AM
Replies: 11
Views: 5,986
Posted By edm1
In case this is useful to anyone in the future;...

In case this is useful to anyone in the future; My problem was that I was running on a Beowolf cluster and the network drive I had my reads on was only available from the login nodes, not the worker...
Forum: General 01-09-2014, 07:35 AM
Replies: 3
Views: 1,414
Posted By edm1
Thanks for the info. It does seem strange. I've...

Thanks for the info. It does seem strange. I've only been doing bioinformatics for 18 months or so and this is the first time I have seen a csfasta.

I got around the problems by using bowtie (v1,...
Forum: General 01-08-2014, 08:16 AM
Replies: 3
Views: 1,414
Posted By edm1
Ah, supposedly it is a colour space fasta with...

Ah, supposedly it is a colour space fasta with some extra info in the header. I have never used SOLiD data before.

Is the colour code for converting to a nucleotide sequence always the same or...
Forum: General 01-08-2014, 07:38 AM
Replies: 3
Views: 1,414
Posted By edm1
What file format is this? [ChIP-seq]

I have been given this file. I know it is genomic co-ordinates for mapped ChIP-seq reads. Is this a standard format?

Example:

>966_1402_741_F3,7_136537485.3,10.34...
Forum: Bioinformatics 11-26-2013, 02:40 AM
Replies: 4
Views: 7,127
Posted By edm1
Thanks. That has greatly improved the feature...

Thanks. That has greatly improved the feature counts:

successfull feature = 15,000,966 (45.3%)
no_feature = 8,715,612 (26.33%)
ambiguous = 172,178 (0.52%)
alignment_not_unique = 9,215,369 ...
Forum: Bioinformatics 11-25-2013, 12:56 PM
Replies: 4
Views: 7,127
Posted By edm1
HTSeq-count large proportion of mapped reads with no_feature

Hi,
I am fairly new to RNA-Seq analysis and hoped someone could help me diagnose the reason why I have such a low proportion of reads mapped to features with my current method.

The experiment:
-...
Showing results 1 to 10 of 10

 


All times are GMT -8. The time now is 06:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO