SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 39
Search took 0.00 seconds.
Search: Posts Made By: tristan dubos
Forum: Illumina/Solexa 03-13-2017, 11:55 PM
Replies: 2
Views: 1,482
Posted By tristan dubos
Hi , I think the "BED files" for WGS you...

Hi ,

I think the "BED files" for WGS you are looking is the genome reference used to align the reads.
Best,

Tristan
Forum: Bioinformatics 03-06-2017, 04:07 AM
Replies: 0
Views: 882
Posted By tristan dubos
Question Error using xhmm

Hi all ,

I am trying to use xhmm to call CNV , but i got the following error on the last step when i m using ./xhmm --discover :

ERROR: Cannot find ':' in target string name_of_one_sample
...
Forum: Bioinformatics 02-23-2017, 05:54 AM
Replies: 15
Views: 3,465
Posted By tristan dubos
Sorry i miss a word i would say i don't know...

Sorry i miss a word i would say i don't know about mac. The think is if i understand right BIG_BIGWIG.py use wigToBigWig to calculate something, and to call it he need to know where is wigToBigWig.
Forum: Bioinformatics 02-23-2017, 04:27 AM
Replies: 15
Views: 3,465
Posted By tristan dubos
It's an exe in linux you have use it using...

It's an exe in linux you have use it using ./wigToBigWig , don't for mac. Same you have to give right to your system to use it and if it's call by BIG_BIGWIG.py you have to had the path to the exe...
Forum: Bioinformatics 02-23-2017, 01:57 AM
Replies: 15
Views: 3,465
Posted By tristan dubos
I think you have to install it

I think you have to install it
Forum: Bioinformatics 02-23-2017, 01:45 AM
Replies: 15
Views: 3,465
Posted By tristan dubos
Well dependency !!! Enjoy !! :) Just a think...

Well dependency !!! Enjoy !! :)
Just a think what is the next step with your bigwig ? Are you making an annotation or something ?
I think you have to install wigToBigWig from UCSC...
Forum: Bioinformatics 02-23-2017, 01:07 AM
Replies: 15
Views: 3,465
Posted By tristan dubos
Hi , What did you try ? it seems to be...

Hi ,

What did you try ? it seems to be something like :
bam_to_wiggle.py Galaxy6RmDupdata.bam --outfile path_to_the_result

Tristan
Forum: Bioinformatics 02-21-2017, 02:01 AM
Replies: 6
Views: 2,267
Posted By tristan dubos
You have to download the zip file and...

You have to download the zip file and uncompressed it and follow the instruction which are in the reads me files. You should care about the dependency :)

Tristan
Forum: Bioinformatics 02-21-2017, 01:50 AM
Replies: 6
Views: 2,267
Posted By tristan dubos
I think if i understand right your problematic is...

I think if i understand right your problematic is which tools you can use to calculate your metrics, isn't it ?
if you want to produce the exactly same result you should use the same tool which...
Forum: Bioinformatics 02-21-2017, 01:08 AM
Replies: 6
Views: 2,267
Posted By tristan dubos
Hi, I'm not sure to understand what you...

Hi,

I'm not sure to understand what you want , do you have sequencing data, in this case is it a bam ? ? or you just want some information about you protein ?

Regards

Tristan
Forum: Ion Torrent 02-16-2017, 10:53 PM
Replies: 1
Views: 2,672
Posted By tristan dubos
Hi, I worked on the Colon and Lung Cancer...

Hi,
I worked on the Colon and Lung Cancer Panel v2 for 1 years , i cant tell you that if DNA is good we can sequence around 300 000 reads per sample (we multiplex 16 samples per run). In still good...
Forum: Bioinformatics 02-16-2017, 02:23 AM
Replies: 2
Views: 1,391
Posted By tristan dubos
Hi , I don't know tools for that (may be in R...

Hi ,
I don't know tools for that (may be in R there's something available) and i think it's more personal scripting code . Anyways i think you can do it with excel and tab links if you don't code,...
Forum: General 02-09-2017, 06:33 AM
Replies: 0
Views: 1,063
Posted By tristan dubos
Problem igvtools count

Hi ,

I would like to detect some genome position indel. So i decide to use igvtools count to extract details for all position sequenced in my 900 dataset. I used for every amplicon this command :...
Forum: Bioinformatics 11-10-2016, 01:06 AM
Replies: 2
Views: 2,365
Posted By tristan dubos
Hi NielQC, You should read...

Hi NielQC,
You should read ftp://ftp.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/README_NIST_Illumina_pairedend_NA12878.txt that will help you to understand :)
It seems...
Forum: General 09-02-2016, 03:47 AM
Replies: 2
Views: 1,158
Posted By tristan dubos
Thank you for the answer. There is not log file...

Thank you for the answer. There is not log file during the conversion (with default mode) i think the log file is create during the annotate_variation.pl
Forum: General 09-02-2016, 12:58 AM
Replies: 2
Views: 1,158
Posted By tristan dubos
Post Annovar variant filtering

He guys,
I m using convert2annovar.pl to convert vcf to avinput , and in this output i have only 14 variants against more then 1000 variants in the input.
Do you know witch filters apply...
Forum: Bioinformatics 08-23-2016, 12:54 AM
Replies: 6
Views: 1,363
Posted By tristan dubos
Hi , to close this subject if somebody is...

Hi ,
to close this subject if somebody is interested in , i find a simple solution. I developed a little pipeline to convert INDELs from Clinvar and dbSNP databases to detect them. I just generated...
Forum: Bioinformatics 08-17-2016, 11:04 PM
Replies: 5
Views: 1,646
Posted By tristan dubos
Hi, You can do it with bwa (it s an aligner)...

Hi,
You can do it with bwa (it s an aligner) who will map your sequencing illumina against your references . You need to modify your references genes with N before and after ( N is considering as...
Forum: Bioinformatics 08-10-2016, 11:09 PM
Replies: 5
Views: 1,646
Posted By tristan dubos
You welcome :) I' am sorry for you but i don't...

You welcome :)
I' am sorry for you but i don't really know a simple solution for that , i mean there no software i know for this specific question. The solution has to be a combination of software...
Forum: Bioinformatics 08-10-2016, 04:06 AM
Replies: 5
Views: 1,646
Posted By tristan dubos
Hi, You can try an assembly of your mutants...

Hi,
You can try an assembly of your mutants genomes and then map your genes references against your references genome created (could be complicate :) ). I know there is some assembler witch start...
Forum: Bioinformatics 08-07-2016, 11:08 PM
Replies: 1
Views: 1,953
Posted By tristan dubos
Hi , I looked the Clustal Omega and you can...

Hi ,
I looked the Clustal Omega and you can only compared homologous by pair ? and the think is how to automatize it ?

Trist
Forum: Bioinformatics 08-04-2016, 03:05 AM
Replies: 2
Views: 1,211
Posted By tristan dubos
Hi, I think it's a good result ! I'm not...

Hi,
I think it's a good result ! I'm not specialist in bacteria but if i remember rigth there is a big diversity in population and the genomic dynamic is intensive ( i speak about bacteria in...
Forum: Bioinformatics 07-28-2016, 11:59 PM
Replies: 2
Views: 2,911
Posted By tristan dubos
Hi, I was with the same problematic when I...

Hi,
I was with the same problematic when I studies repeats region to determine number copy. I saw in BWA(mem) no mapping to the extremity of my reference (500 bases). To solve the problem by put 2...
Forum: Bioinformatics 07-20-2016, 01:45 AM
Replies: 2
Views: 2,109
Posted By tristan dubos
Hi Guillaume, The correction appends if...

Hi Guillaume,

The correction appends if there is a better alignment possible, how do you know you should have a different alignment in this position ?

Tristan
Forum: Bioinformatics 06-28-2016, 11:55 PM
Replies: 6
Views: 1,363
Posted By tristan dubos
Thank you for your answers. I understand you...

Thank you for your answers. I understand you point of view it an option to annotate one by one INDEL and check if it exists in dbSNP or other database. I am still surprise that nobody already creates...
Showing results 1 to 25 of 39

 


All times are GMT -8. The time now is 10:38 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO