Forum: Bioinformatics
08-11-2015, 12:01 PM
|
|
Replies: 5
Views: 4,332
Hi donquijotes,
Sorry for a late reply, I'm...
Hi donquijotes,
Sorry for a late reply, I'm not checking this forum very often.
First, in our practice we integrate UMIs using RT-PCR template-switching. We don't see a severe synthesis biases...
|
|
Forum: Bioinformatics
11-24-2014, 09:07 AM
|
|
Replies: 31
Views: 14,090
Hello!
DRIVER_PROB means the probability (in...
Hello!
DRIVER_PROB means the probability (in Bayesian sense) of being a driver mutation.
The same in represented by P-value, the probability of being a passanger, with one major difference....
|
|
Forum: Bioinformatics
09-10-2014, 05:53 AM
|
|
Replies: 31
Views: 14,090
Hello!
Both initially are Bayesian...
Hello!
Both initially are Bayesian probabilities. The first one is probability of being a passenger (class 0), the second a driver (class 1), with the sum of them being 1. As usually RNA-Seq...
|
|
Forum: Bioinformatics
04-11-2014, 03:24 AM
|
|
Replies: 7
Views: 3,072
Dear all!
Here is a link to binary...
Dear all!
Here is a link to binary distribution of MiTCR with support of gamma-delta genes:
http://files.milaboratory.com/mitcr/1.0.3.1-beta/mitcr.jar
As we didn’t release it yet, the only...
|
|
Forum: Bioinformatics
04-10-2014, 12:53 PM
|
|
Replies: 7
Views: 3,072
|
|
Forum: Bioinformatics
04-10-2014, 10:35 AM
|
|
Replies: 7
Views: 3,072
|
|
Forum: Bioinformatics
04-10-2014, 09:32 AM
|
|
Replies: 7
Views: 3,072
Well to the best of my knowledge there are...
Well to the best of my knowledge there are currently no tools able to efficiently process huge amounts of TCR repertoire sequencing data.
If you simply need to do this for several sequences...
|
|
Forum: Bioinformatics
02-09-2014, 06:41 AM
|
|
Replies: 6
Views: 3,644
In this case I'd rather use statistical testing...
In this case I'd rather use statistical testing for functional enrichment and selected differentially expressed (DE) genes by fold-change. I would select several DE gene lists with e.g. 1.5-, 2- and...
|
|
Forum: General
01-12-2014, 08:35 AM
|
|
Replies: 9
Views: 6,669
|
|
Forum: General
01-12-2014, 05:35 AM
|
|
Replies: 4
Views: 3,000
Variable, Diversity and Joining segments data
Ok just as promised (sorry for a delay due to holidays). Here are the lists of segments for TRA/B/G/D and IGH/K/L genes of human and mice.
They were originally filtered from IMGT data. The script...
|
|
Forum: General
12-19-2013, 02:54 AM
|
|
Replies: 4
Views: 3,000
|
|
Forum: Bioinformatics
12-17-2013, 04:00 AM
|
|
Replies: 4
Views: 2,813
As far as I remember, -num_threads option is...
As far as I remember, -num_threads option is actually not working as expected, and blast runs in a single thread most of time. What I usually do (for the same type of problem): split query to...
|
|
Forum: Bioinformatics
11-15-2013, 01:33 PM
|
|
Replies: 16
Views: 10,682
Go to UCSC GB, browse the tables and download...
Go to UCSC GB, browse the tables and download RefGene track. It has genomic coordinates and "name2" field that is a HGNC gene symbol. Of course each gene could have several transcripts (NM_*...
|
|
Forum: Bioinformatics
10-19-2013, 03:43 AM
|
|
Replies: 24
Views: 10,103
Well it is still possible to do transcriptome...
Well it is still possible to do transcriptome assembly with Trinity on 64Gb RAM, just have to do several tricks, like increasing min k-mer count for Inchworm.
Also agree that Minia the best...
|
|
Forum: Metagenomics
10-10-2013, 12:55 PM
|
|
Replies: 4
Views: 2,958
Actually there are many tools for gene ontology...
Actually there are many tools for gene ontology enrichment analysis. You can also simply use hypergeometric tests with some multiple testing correction (eg Bonferrony), or check out EASE framework...
|
|
Forum: Metagenomics
10-09-2013, 12:54 PM
|
|
Replies: 4
Views: 2,958
|
|
Forum: Bioinformatics
10-07-2013, 12:08 AM
|
|
Replies: 8
Views: 4,862
Generally speaking, if there is a sequencing...
Generally speaking, if there is a sequencing error you cannot get rid of it if you'll sequence deeper. And 75x seems enough.
Some control, i.e. known mutation in tumor is desirable to fine-tune your...
|
|
Forum: Bioinformatics
10-06-2013, 02:47 PM
|
|
Replies: 7
Views: 5,169
|
|
Forum: Bioinformatics
09-14-2013, 04:45 PM
|
|
Replies: 31
Views: 14,090
Indeed, for a patient sample it could be...
Indeed, for a patient sample it could be meaningless. The examples from Tophat-fusion pages don't contain any contradictory reads, but they are derived from homogenous cell lines. Patient samples...
|
|
Forum: Bioinformatics
09-04-2013, 01:31 AM
|
|
Replies: 31
Views: 14,090
|
|
Forum: Bioinformatics
09-03-2013, 06:05 AM
|
|
Replies: 31
Views: 14,090
|
|
Forum: Bioinformatics
09-03-2013, 03:13 AM
|
|
Replies: 31
Views: 14,090
The new version will be uploaded to home page...
The new version will be uploaded to home page later in the day.
I've fixed the URL, it is: https://s3-eu-west-1.amazonaws.com/oncofuse/oncofuse-v1.0.3.zip. There seems to be some trouble with URL...
|
|
Forum: Bioinformatics
09-03-2013, 02:42 AM
|
|
Replies: 31
Views: 14,090
|
|
Forum: Bioinformatics
09-02-2013, 03:26 PM
|
|
Replies: 31
Views: 14,090
|
|
Forum: Bioinformatics
09-02-2013, 07:00 AM
|
|
Replies: 31
Views: 14,090
|
