User: flappix

gravatar for flappix
flappix30
Reputation:
30
Status:
New User
Location:
Last seen:
6 days, 7 hours ago
Joined:
1 year, 10 months ago
Email:
f**********@fu-berlin.de

Posts by flappix

<prev • 7 results • page 1 of 1 • next >
1
vote
0
answers
138
views
0
answers
Comment: C: Extract list of gene coordinates from gff file
... Try to make your regex as specific as possible. E.g. `grep GSBRNA2T00155995001 sample.gtf` will be slightly slower than `grep 'gene_id \"GSBRNA2T00155995001' sample.gtf`. How much improvement you can gain from this depends on the structure of your gtf file. ...
written 4 weeks ago by flappix30
0
votes
1
answer
139
views
1
answers
Comment: C: Gene alignment with IGV
... Thanks for your suggestion. I tried this but I was not able to get a reasonable alignment with bwa. I think these programs are designed to map short reads against a large reference genome and not to align two (somewhat) similar genes. ...
written 4 weeks ago by flappix30
0
votes
1
answer
139
views
1
answers
Comment: C: Gene alignment with IGV
... Thanks for your suggestion. Unfortunately one can only use this feature if the genome is available in the UCSC genome browser which is not the case (or one have to setup its own Blat server, but that's a bit of an overkill). Nevertheless it's good to know this feature exists in case I face this pr ...
written 4 weeks ago by flappix30
3
votes
1
answer
139
views
1
answer
Gene alignment with IGV
... Hi, I have loaded a genome and a gtf file into IGV to see the intron/exon structure of a gene. Now I want to align a sequence against this gene and see which parts of the sequence are falling into introns and exons of the gene. Which program would be best to create the alignment in way IGV can re ...
alignment igv written 4 weeks ago by flappix30
0
votes
2
answers
1.9k
views
2
answers
Comment: C: [limma] LogFC interpretation
... Thank you very much, I see my mistake. Just to be sure: If I want to retrieve the absolute expression values, I have to use ```2^exprs(results)``` ? ...
written 21 months ago by flappix30
6
votes
2
answers
1.9k
views
2
answers
[limma] LogFC interpretation
... Hi @ all, I have cel files from 2 groups, 3 replicates each group. I want to use limma for the differential gene expression analysis. My script looks like this prefix = "101053-0" cels <- ReadAffy ( filenames = paste ( paste (prefix, c(4,5,6,1,2,3), sep=""), ".CEL", sep="" ), ...
R microarray logfc limma written 21 months ago by flappix30 • updated 21 months ago by zx87549.3k
0
votes
0
answers
489
views
0
answers
strange intensity decay plot
... Hi, I got 6 cel files from an Affymetrix microarray experiment: two conditions and 3 replicates of each condition. I used the function `plotDx` from the R package AffyRNADegradation to review the rna degradation and this is what I got: ![intensity decay plot][1] 101053-01, 101053-02, 101053-03 ar ...
microarray rna degradation written 22 months ago by flappix30

Latest awards to flappix

Popular Question 21 months ago, created a question with more than 1,000 views. For [limma] LogFC interpretation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1380 users visited in the last hour