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Search: Posts Made By: AJERYC
Forum: Bioinformatics 09-14-2015, 12:50 PM
Replies: 1
Views: 1,430
Posted By AJERYC
I've got the same error message when trying to...

I've got the same error message when trying to get a pairwise model estimateGLMCommonDisp. My mistake was with the design matrix.
If you type on R

>?estimateGLMCommonDisp

you get a full...
Forum: Bioinformatics 12-09-2014, 11:45 AM
Replies: 3
Views: 1,379
Posted By AJERYC
There is a tool called samstats that looks for a...

There is a tool called samstats that looks for a very common chain in your sequences. Try to run it and it will show you your adapters sequence
Forum: Bioinformatics 02-26-2014, 11:55 PM
Replies: 3
Views: 1,024
Posted By AJERYC
You can use the extra genotyped individual to add...

You can use the extra genotyped individual to add information. For example you can use kggseq with a recessive study option:

java -jar ./kggseq.jar --buildver hg19 --vcf-file path/to/file1...
Forum: Clinical Sequencing 01-10-2014, 05:41 AM
Replies: 4
Views: 12,902
Posted By AJERYC
Alzheimer's disease-gene database list

The alzgene database contains the results of GWAS studies on Alzheimer's disease. If you wanted the mutations of main genes involved in dementia look in AD&FTD mutation database...
Forum: Bioinformatics 04-09-2013, 04:43 AM
Replies: 11
Views: 3,394
Posted By AJERYC
try kggseq java -Xms256m -Xmx1300m...

try kggseq

java -Xms256m -Xmx1300m --buildver hg19 -jar kggseq.jar --no-resource-check --buildver hg19 --vcf-file yourfile.vcf --ped-file pedigree.ped --o-vcf --genotype-filter 2,4

in file...
Forum: Bioinformatics 04-03-2013, 11:33 PM
Replies: 6
Views: 9,719
Posted By AJERYC
Not sure if it is the same for RNA, but this is...

Not sure if it is the same for RNA, but this is what I do for DNA. I hope you can get some hints from it:
First you need a reference genome, for example hg19 for human DNA. Second, install properly...
Forum: Bioinformatics 04-01-2013, 11:22 PM
Replies: 0
Views: 1,148
Posted By AJERYC
kggseq under proxy

Hi,
I'm trying to run KGGSeq under proxy but can't connect to the internet to get new resources.
I have tried the:

java -Dhttp.proxyHost=xxx.xxx.xxx -Dhttp.proxyPort=xxxx -Dhttp.proxyUser=xxx...
Forum: Bioinformatics 03-25-2013, 06:42 AM
Replies: 6
Views: 1,660
Posted By AJERYC
(SOLVED) Thanks for backup. This is what worked...

(SOLVED) Thanks for backup. This is what worked for me: in R:
install.packages("RHmm")

Installing package(s) into ‘~/R/x86_64-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified)
--- Please...
Forum: Bioinformatics 03-25-2013, 05:28 AM
Replies: 6
Views: 1,660
Posted By AJERYC
This is what the paper recommends: >...

This is what the paper recommends:
> install.packages("RHmm", repos="http://R-Forge.R-project.org")
Alternatively, the package can be downloaded from homepage of the RHmm project at R-Forge1 It can...
Forum: Bioinformatics 03-25-2013, 05:12 AM
Replies: 6
Views: 1,660
Posted By AJERYC
Yes, both are already installed.

Yes, both are already installed.
Forum: Bioinformatics 03-25-2013, 04:27 AM
Replies: 6
Views: 1,660
Posted By AJERYC
R module RHmm for ibd2.r script

I'm trying to run the R script ibd2.R in order to perform IBD=2 analysis on exome sequences (Bioinformatics. 2011 Mar 15;27(6):829-36. 2011 Jan 28. Identity-by-descent filtering of exome sequence...
Forum: General 03-10-2013, 12:43 AM
Replies: 1
Views: 1,554
Posted By AJERYC
The best way to confirm your hypothesis would be...

The best way to confirm your hypothesis would be to have several tumor samples were homozygous or heterozygous that you can use as controls in your experiments. This could be possible since the...
Forum: Bioinformatics 12-16-2012, 07:17 AM
Replies: 1
Views: 3,106
Posted By AJERYC
That its an error that appears when you are...

That its an error that appears when you are working with very large files. It has to do with linux or windows handling of ram memory
Forum: Genomic Resequencing 11-23-2012, 07:19 AM
Replies: 6
Views: 2,550
Posted By AJERYC
[QUOTE=albertyu;89712]Indeed, all my female...

[QUOTE=albertyu;89712]Indeed, all my female samples have chrY variations.
From my data performed by GATK, it separated substitutions and indels. So I originally thought those are all indels and...
Forum: Genomic Resequencing 11-09-2012, 02:20 AM
Replies: 8
Views: 4,260
Posted By AJERYC
[QUOTE=gensdei;88907]Cell lines have the benefit...

[QUOTE=gensdei;88907]Cell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper...
Forum: Bioinformatics 11-08-2012, 06:05 AM
Replies: 2
Views: 1,800
Posted By AJERYC
I dont think LOD score would be useful in this...

I dont think LOD score would be useful in this regard since you would need a very extensive family unless you are studying a recessive disorder Besides with NGS you get so many data that would...
Forum: Bioinformatics 09-21-2012, 06:55 AM
Replies: 13
Views: 3,275
Posted By AJERYC
for me it had worked if you put "perl" at the...

for me it had worked if you put "perl" at the start of the sentence provided that you have perl in the path. e.g.
perl summarize_annovar.pl -buildver hg19 inputsnp.human humandb/ -outfile...
Forum: Bioinformatics 09-21-2012, 06:54 AM
Replies: 13
Views: 3,275
Posted By AJERYC
for me it had worked if you put "perl" at the...

for me it had worked if you put "perl" at the start of the sentence if you have perl in the path. e.g.
perl summarize_annovar.pl -buildver hg19 inputsnp.human humandb/ -outfile summarizeoutput
Forum: Bioinformatics 09-20-2012, 07:08 AM
Replies: 138
Views: 70,096
Posted By AJERYC
I think the error is here: Couldn't write file...

I think the error is here:
Couldn't write file E:\EXOME DATA ANALYSIS\1 Unzipped fastq
check up for Linux write permissions of the directory, harddisk space...
Forum: Bioinformatics 09-06-2012, 11:13 PM
Replies: 138
Views: 70,096
Posted By AJERYC
I'm not sure if we are running the same version...

I'm not sure if we are running the same version of GATK. For Quality score recalibration I use the following instructions

java -Xmx16G -jar gatk/GenomeAnalysisTK.jar -I...
Forum: Bioinformatics 09-06-2012, 05:17 AM
Replies: 138
Views: 70,096
Posted By AJERYC
This error messages means these sequences can not...

This error messages means these sequences can not be aligned against the reference genome. That is why you use the VALIDATION_STRINGENCY=LENIENT option so that the programs points you the sequences...
Forum: Bioinformatics 09-05-2012, 04:00 AM
Replies: 138
Views: 70,096
Posted By AJERYC
IOException: No space left on device

I have got the same errors and it seems I ran out of space in the hard drive. If you are running a very large exome file (i.e. 100 x exome) you may need a large space for your temporary files. Try to...
Forum: General 08-22-2012, 05:29 AM
Replies: 1
Views: 4,546
Posted By AJERYC
discrepancies in allele frequencies between 1000 genomes and 5400 exomes

Using ANNOVAR summary routine I have got a exome_summary.csv file that contains different columns with 1000 genomes and 5400 exomes frequencies with some empty cells. I asume that empty cells...
Forum: Bioinformatics 05-05-2012, 12:03 PM
Replies: 1
Views: 1,117
Posted By AJERYC
how can I get the exome sequencing

Sorry if this question may sound very simple, but I cant find the solution. I have a SAM file with an exome sequencing, all the short ILUMINA sequences aligned. I know how to get the variant file...
Forum: Genomic Resequencing 05-05-2012, 11:56 AM
Replies: 8
Views: 4,260
Posted By AJERYC
30x is definitely not enough, since it means 30x...

30x is definitely not enough, since it means 30x averge, so you will get a lot of regions with very few sequences, that will make impossible for you to resolve heterozygous mutations. Go 50x or 100x.
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