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Search: Posts Made By: svl
Forum: Bioinformatics 08-14-2012, 02:42 AM
Replies: 3
Views: 1,500
Posted By svl
That does the job indeed. Afterwards index the...

That does the job indeed. Afterwards index the new BAM file (samtools index) and you're good to go.

I get the tty warning as well, doesn't seem to be any problem..
Forum: Bioinformatics 07-10-2012, 03:03 AM
Replies: 2
Views: 1,929
Posted By svl
Maybe this can help you: ...

Maybe this can help you:
http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage_v3.0

Requires some work to get it working properly and also I think the documentation is not that clear...
Forum: Bioinformatics 12-29-2011, 07:51 AM
Replies: 3
Views: 1,097
Posted By svl
Hi Filippo, haven't tried this myself but perhaps...

Hi Filippo, haven't tried this myself but perhaps you can use SortSam in Picard tools:

http://picard.sourceforge.net/command-line-overview.shtml#SortSam

Why do you want this specific order in...
Forum: Bioinformatics 09-07-2011, 06:06 AM
Replies: 7
Views: 2,817
Posted By svl
I'm still looking at an efficient way to do this...

I'm still looking at an efficient way to do this too. I use samtools view and perl to create a table for each sample (.bam) with for each region (so in this case exon coordinates):

- average...
Forum: Bioinformatics 02-09-2011, 11:31 PM
Replies: 5
Views: 3,869
Posted By svl
Hi Sneha, Here's the documentation of the...

Hi Sneha,

Here's the documentation of the api:
http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

There is example code for perl, ruby, python and java.

/Stef
Forum: Bioinformatics 10-27-2010, 08:36 AM
Replies: 4
Views: 3,996
Posted By svl
Are you using bioconductor?

This should be doable with bioconductor as well.

How to install bioconductor:
source(“http://www.bioconductor.org/biocLite.R”)
biocLite()

How to create an aligment:...
Forum: Bioinformatics 10-23-2010, 08:26 AM
Replies: 40
Views: 13,737
Posted By svl
If you mean how to get the consequence of a...

If you mean how to get the consequence of a variation (whether it's a SNV or a small INDEL) -> we use the ensembl snp effect predictor:

http://www.ensembl.org/tools.html

When using the ensembl...
Forum: Bioinformatics 10-23-2010, 08:16 AM
Replies: 1
Views: 788
Posted By svl
Looking for something like this?...

Looking for something like this?...
Forum: General 10-23-2010, 08:06 AM
Replies: 2
Views: 1,289
Posted By svl
What do you want to do with NGS (eg calling...

What do you want to do with NGS (eg calling variants)? Which technology will you be using (eg illumina)?

For a start, a list of software:
http://seqanswers.com/wiki/Special:BrowseData
Forum: Bioinformatics 10-03-2010, 02:06 AM
Replies: 13
Views: 9,917
Posted By svl
One option (but perhaps not the most complete) is...

One option (but perhaps not the most complete) is to use the Ensembl SnpEffectPredictor script:
ftp://ftp.ensembl.org/pub/misc-scripts/SNP_effect_predictor_1.0/

There is also an online version...
Forum: Bioinformatics 09-27-2010, 02:39 PM
Replies: 23
Views: 11,212
Posted By svl
Maybe the alignment view of IGV is enough for...

Maybe the alignment view of IGV is enough for want you want, it has a coverage track:
http://www.broadinstitute.org/igv/AlignmentData

For a completely different idea you could also have a look at...
Forum: Bioinformatics 09-27-2010, 04:21 AM
Replies: 8
Views: 10,853
Posted By svl
Hi yuanzhi, I've found the performance and...

Hi yuanzhi,

I've found the performance and errors of polyphen2 confusing as well. But for your genomic positions it might be because they are not in protein coding sequence (I only checked your...
Forum: Genomic Resequencing 09-21-2010, 01:42 PM
Replies: 2
Views: 3,067
Posted By svl
What exactly do you want to visualize? If think...

What exactly do you want to visualize? If think you want to see the mapped reads and where they differ from reference (known/possible SNPs) as stacked output (so all complete reads!)... If so you...
Forum: Bioinformatics 09-20-2010, 02:35 PM
Replies: 7
Views: 13,320
Posted By svl
Never used/tested it myself but the google search...

Never used/tested it myself but the google search "gtf2bed" came up with: http://noble.gs.washington.edu/~shobhitg/proj/hs/bin/gtf2bed

If you know how to use a perl script you might want to try...
Forum: Illumina/Solexa 09-20-2010, 02:28 PM
Replies: 2
Views: 1,626
Posted By svl
Are you sure this is not the input format? I've...

Are you sure this is not the input format? I've never used Novoalign, but when mapping you normally use fastq as input and SAM/BAM as output (as is stated on the novoalign website as well...) A...
Forum: Bioinformatics 09-17-2010, 04:05 AM
Replies: 12
Views: 3,464
Posted By svl
We do not use "on target reads" but "on target...

We do not use "on target reads" but "on target bases". From all mapped reads the percentage of bases "on target" is determined. So if a read overlaps "target region" for 10%, it contributes 10%. And...
Forum: Bioinformatics 09-16-2010, 01:34 PM
Replies: 1
Views: 1,651
Posted By svl
Thanks god yes ;) Since you're already...

Thanks god yes ;)


Since you're already using SAMTOOLS, have a look at the pileup command/format: http://samtools.sourceforge.net/pileup.shtml One of the columns shows whether the reads...
Forum: Bioinformatics 09-16-2010, 07:11 AM
Replies: 12
Views: 3,464
Posted By svl
Here as well. Using solid: 65-70 % of bases (of...

Here as well. Using solid: 65-70 % of bases (of mappable reads) are on target.
Forum: General 09-13-2010, 02:22 PM
Replies: 1
Views: 3,884
Posted By svl
Maybe galaxy has what you're looking for: ...

Maybe galaxy has what you're looking for:
http://main.g2.bx.psu.edu/

Or fastqc:
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

Or have a look at the wiki:...
Forum: Bioinformatics 09-13-2010, 02:05 PM
Replies: 13
Views: 6,410
Posted By svl
One possibility: 1. align with BWA 2. get...

One possibility:
1. align with BWA
2. get variation with SAMTOOLS pileup

http://bio-bwa.sourceforge.net/
http://samtools.sourceforge.net/cns0.shtml
Forum: Bioinformatics 09-10-2010, 07:02 AM
Replies: 4
Views: 1,811
Posted By svl
The format of the fastq files should be equal, I...

The format of the fastq files should be equal, I guess..? Do you mean the different quality value encoding? If so, here is a description:
http://en.wikipedia.org/wiki/FASTQ_format#Encoding

You...
Forum: Bioinformatics 09-09-2010, 12:51 PM
Replies: 6
Views: 4,984
Posted By svl
Hi Ramet, At this link you can find txt...

Hi Ramet,

At this link you can find txt files with the info you need, although I'm not sure what the "lvl" is...
http://www.geneontology.org/GO.downloads.files.shtml

You can write a small perl...
Forum: SOLiD 08-17-2010, 01:48 AM
Replies: 4
Views: 1,844
Posted By svl
The pileup command in SAMTOOLS can be used for...

The pileup command in SAMTOOLS can be used for generating position-based output and consensus/indel calling.
http://samtools.sourceforge.net/pileup.shtml

update:
I now realize you probably mean...
Forum: Genomic Resequencing 08-10-2010, 02:41 AM
Replies: 5
Views: 2,497
Posted By svl
It could be a heterozygous SNP. Also errors...

It could be a heterozygous SNP. Also errors can/will always occur (in sequencing, mapping), you might want to look at quality values as well.
Forum: Bioinformatics 08-01-2010, 07:01 AM
Replies: 5
Views: 3,869
Posted By svl
Thanks for the help, BioSlayer, I've decided to...

Thanks for the help, BioSlayer, I've decided to just download txt DBs with the pathway information as using the API could get really slow for the hundreds of genes I would like to query the DB...
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