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Forum: Bioinformatics 03-21-2013, 07:50 AM
Replies: 0
Views: 830
Posted By fadista
correction for gene length in burden tests

Hi,

I would like to know if any of the gene rare variant burden tests out there tries to correct for gene length, or number of variants per gene.
As far as I know (might be wrong) this doesn´t...
Forum: General 12-21-2012, 05:36 AM
Replies: 0
Views: 954
Posted By fadista
burden tests

Hi,

I would like to know if anyone knows of a sequencing association test for rare variant effects that can detect an enrichment of variants as we go up in the values of phenotype X stratified...
Forum: General 12-16-2012, 06:50 AM
Replies: 4
Views: 1,118
Posted By fadista
Perfect. Thanks a lot for Mauve

Perfect. Thanks a lot for Mauve
Forum: General 12-13-2012, 03:50 AM
Replies: 4
Views: 1,118
Posted By fadista
Yes, I was looking for a software where I was...

Yes, I was looking for a software where I was able to detect differences in assembly like duplications, inversions, expansions quite easily in a 2 Mb window or so...
Forum: General 12-12-2012, 09:02 AM
Replies: 4
Views: 1,118
Posted By fadista
visualizing differences between gneome builds

Hi,

I know you have the remap tool to map genomic coordinates between different builds, but I was wondering if there is any visualizing tool that I can use to compare the assembly of small region...
Forum: General 11-29-2012, 03:30 PM
Replies: 0
Views: 2,234
Posted By fadista
convert plink files to VCF

Hi,

I would like to know if anyone has a script/tool to convert plink .map and .ped files into VCF.

We should have in mind that for instance a genotype in the .ped file could be AG, but this...
Forum: Bioinformatics 07-09-2012, 07:11 AM
Replies: 1
Views: 1,232
Posted By fadista
junctions usage

Dear all,

I would like to know if there is a tool out there that can handle the junctions file coming out from Cufflinks and treat them as for instance the DEXSeq Bioconductor package, but instead...
Forum: Bioinformatics 06-27-2012, 01:59 AM
Replies: 14
Views: 3,642
Posted By fadista
I got the same error message here. Did you find...

I got the same error message here. Did you find any solutions?

Thanks.
Forum: Bioinformatics 01-04-2012, 03:00 AM
Replies: 4
Views: 8,649
Posted By fadista
Thanks for the replies. The input was 10pM...

Thanks for the replies.

The input was 10pM and with that amount of reads I guess I would have a mean exome coverage of around 134 fold (assuming all PF reads align):
(82461815reads *...
Forum: Bioinformatics 01-03-2012, 05:59 AM
Replies: 4
Views: 8,649
Posted By fadista
fastqc sequence duplication level

Hi,

I was wondering if it is normal to have a fastqc plot with sequence duplication level around 60% for a high depth human exome sequencing (82 461 815 reads, or 41230908*2 paired-end reads)
Forum: General 12-21-2011, 05:37 AM
Replies: 13
Views: 10,109
Posted By fadista
ExomeCNV

Hi,

I would suggest ExomeCNV: http://bioinformatics.oxfordjournals.org/content/early/2011/08/09/bioinformatics.btr462
Forum: Bioinformatics 12-19-2011, 01:58 PM
Replies: 0
Views: 1,394
Posted By fadista
region of significant allele sharing

Hi,

I would like to know if anyone knows of any tool that retrieves from a multi-sample .vcf file a query such as: all the genomic regions smaller than 3kb that have >=22 variants (of at least...
Forum: Bioinformatics 12-16-2011, 02:06 AM
Replies: 12
Views: 20,456
Posted By fadista
Does this sff_extract can handle multiplex files?...

Does this sff_extract can handle multiplex files? I have 48individuals/run on a Roche 454 junior and I would like to demultiplex the sff files.

Thanks.
Forum: Bioinformatics 12-01-2011, 10:20 AM
Replies: 2
Views: 2,940
Posted By fadista
multiplex few variants in hundreds of samples

Dear all,

I would like to know if someone is working (or knows someone that is working) on a method to be able to multiplex sequencing of very few variants (let say 100 SNPs) on hundreds or maybe...
Forum: Bioinformatics 10-18-2011, 07:14 AM
Replies: 1
Views: 2,136
Posted By fadista
exome sequencing - big coverage differences

Hi,

I would like to know if any of you had experience with Tru-Seq exome sequencing and if you see that there is a lot of variation in genome coverage between the samples, even within the same...
Forum: Illumina/Solexa 10-17-2011, 01:44 AM
Replies: 0
Views: 1,909
Posted By fadista
exome sequencing - big coverage differences

Hi,

I would like to know if any of you had experience with Tru-Seq exome sequencing and if you see that there is a lot of variation in genome coverage between the samples, even within the same...
Forum: General 02-15-2011, 11:11 PM
Replies: 3
Views: 8,332
Posted By fadista
Thanks for the replies. I would look into the...

Thanks for the replies. I would look into the mauve tool.

By being a 'better' local de novo assembly vs. reference assembly, I consider a region on the genome that has many SNPs, indels, etc....
Forum: General 02-15-2011, 12:11 AM
Replies: 3
Views: 8,332
Posted By fadista
de novo assembly vs. reference assembly

Hi,

I would like to know if someone has experience in comparing a local de novo assembly to a reference assembly and measure which one is the best.

I have mapped genomic Illumina reads to a...
Forum: Bioinformatics 10-29-2010, 11:00 AM
Replies: 1
Views: 1,832
Posted By fadista
break genome in 44bp reads

Hi,

I would like to know if anyone has a perl or python script to break a genome sequence into 44-bp reads (sliding window of 1bp) in fasta format. Thanks in advance.
Forum: General 02-10-2010, 03:28 PM
Replies: 1
Views: 1,405
Posted By fadista
align to different ref assembly

Hi,

I would like to know if someone have tried to map WGS Illumina reads from one species to a reference assembly from other species (like with 20million years divergence). And if so, what were...
Forum: Bioinformatics 10-07-2009, 10:35 AM
Replies: 0
Views: 1,452
Posted By fadista
indels from MAQ

Hi,

I would like to know if the function indelpe from MAQ as a upper limit of how big can it call an indel? Is it the 'size of the read-1bp' or is it smaller?

Thanks in advance.
Forum: Bioinformatics 07-06-2009, 01:37 AM
Replies: 40
Views: 61,253
Posted By fadista
alignment of bisulfite treated reads

Hi,

I would like to know if any of the available next-gen alignment algorithms like maq, bwa, bowtie or others are able to align bisulfite treated reads from a methylation-seq experiment.

This...
Forum: General 05-11-2009, 12:42 AM
Replies: 1
Views: 2,051
Posted By fadista
alignable portion of a genome

Hi,

I would like to know of a good and fast way that could help me calculate the alignable portion of a genome (not human), given a reference sequence.
When I say alignable portion I mean that I...
Forum: Bioinformatics 05-07-2009, 09:45 AM
Replies: 0
Views: 1,100
Posted By fadista
maq rmdup command

Hi,

I have a question concerning the maq rmdup command file that remove pairs with identical outer coordinates. With the solexa pipeline version 1.3, the name of the reads are not a unique string,...
Forum: Bioinformatics 03-30-2009, 11:31 PM
Replies: 3
Views: 2,475
Posted By fadista
sol2sanger

Hi,

Just want to be sure here:

1 - Is the sol2sanger function of maq 0.7.1 not working for solexa pipeline 1.3?

2 - If not, how can I convert the scores that I already computed...
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