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Search: Posts Made By: mikesh
Forum: Bioinformatics 08-11-2015, 12:01 PM
Replies: 5
Views: 4,332
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
MiTCR web page is up and running

MiTCR web page is up and running
Forum: Bioinformatics 04-10-2014, 10:35 AM
Replies: 7
Views: 3,072
Posted By mikesh
I see :) We're having some maintenance issues, it...

I see :) We're having some maintenance issues, it will be running soon. I'll post here when it will be up
Forum: Bioinformatics 04-10-2014, 09:32 AM
Replies: 7
Views: 3,072
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
As a Russian, I would like to ask you to explain,...

As a Russian, I would like to ask you to explain, what do you mean under "excessive number of Russians in NCBI". I would like to note that there are 185 ethnic groups in Russian Federation today (and...
Forum: General 01-12-2014, 05:35 AM
Replies: 4
Views: 3,000
Posted By mikesh
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
Posted By mikesh
Just at a glance, here is the list of HLA genes...

Just at a glance, here is the list of HLA genes in RefSeq
HLA-F
HLA-F-AS1
HLA-F
HLA-G
HLA-H
HLA-A
HLA-J
HLA-L
HLA-E
Forum: Bioinformatics 12-17-2013, 04:00 AM
Replies: 4
Views: 2,813
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
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
Posted By mikesh
As far as I know MetAMOS also finds ORFs and...

As far as I know MetAMOS also finds ORFs and annotates them using BLAST. After that you should get GO terms for matched proteins and do your GO enrichment tests.
Forum: Bioinformatics 10-07-2013, 12:08 AM
Replies: 8
Views: 4,862
Posted By mikesh
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
Posted By mikesh
I had the same problem. Fixed by rolling back to...

I had the same problem. Fixed by rolling back to previous version of BEDtools, the one from the CONTRA package.
Forum: Bioinformatics 09-14-2013, 04:45 PM
Replies: 31
Views: 14,090
Posted By mikesh
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
Posted By mikesh
I meant that Oncofuse is for functional analysis...

I meant that Oncofuse is for functional analysis and that the confidence that fusion is present in sample at all should be first evaluated from the distribution of mapped reads.
Of course it is a...
Forum: Bioinformatics 09-03-2013, 06:05 AM
Replies: 31
Views: 14,090
Posted By mikesh
It seems that tophat-fusion-post thresholds are...

It seems that tophat-fusion-post thresholds are more soft, like
awk '$5>1&&$6>3&&$8==0'. The selection of fusions that are detected in sample is the task that should be solved by fusion detection...
Forum: Bioinformatics 09-03-2013, 03:13 AM
Replies: 31
Views: 14,090
Posted By mikesh
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
Posted By mikesh
I've checked the file you've uploaded. It was...

I've checked the file you've uploaded. It was indeed the problem that I've mentioned (lack of expression data for some protein interaction partners). The package that I've shared...
Forum: Bioinformatics 09-02-2013, 03:26 PM
Replies: 31
Views: 14,090
Posted By mikesh
One moment :) I've tried to debug these and these...

One moment :) I've tried to debug these and these turned to be several protein interaction partners that don't have associated expression data (not present in Affy array). Check out the package at...
Forum: Bioinformatics 09-02-2013, 07:00 AM
Replies: 31
Views: 14,090
Posted By mikesh
It was actually a packaging problem - all tissue...

It was actually a packaging problem - all tissue types are upper-cased in the script (even if they are lowercase in command line or input file) so all directory names should be upper-cased. I'll...
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