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Search: Posts Made By: IonTom
Forum: Bioinformatics 11-08-2016, 07:51 AM
Replies: 2
Views: 1,257
Posted By IonTom
From my experience Rank Product test gives much...

From my experience Rank Product test gives much better and reliable results than most parametric methods.

To your question. You should limit both microarrays to the probes that are available on...
Forum: Bioinformatics 08-13-2015, 12:45 AM
Replies: 7
Views: 2,458
Posted By IonTom
Normalizing Read Coverage

Dear All,

I would like to compare read depth between two sets of samples
for targeted amplicon regions. Now i would like to normalize all
samples to make their read depth comparable. Which...
Forum: General 05-14-2015, 03:08 PM
Replies: 33
Views: 9,437
Posted By IonTom
So subjunc is now able to find non canonical...

So subjunc is now able to find non canonical junctions ?
Does this influence the aligment ?

Because the subjunc help still says:

Subjunc requires donor/receptor sites to be present when...
Forum: RNA Sequencing 05-14-2015, 02:23 PM
Replies: 14
Views: 5,830
Posted By IonTom
I have a similar problem both for sorted and...

I have a similar problem both for sorted and unsorted output from star.
featurecounts resorts the bam. For the file in question feature count reports 1 read has missing mates. I thought STAR does...
Forum: Bioinformatics 05-14-2015, 02:13 AM
Replies: 1
Views: 638
Posted By IonTom
Arabidopsis

Just a question cocerning Arabidopsis annotation.

When id download the annotation from Ensembl
http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index

i use ...
Forum: Bioinformatics 05-14-2015, 02:03 AM
Replies: 330
Views: 114,497
Posted By IonTom
Dear Brian, i just started using BBduk and...

Dear Brian,

i just started using BBduk and am really happy with it.

There is just a question concerning RNASeq from the NextSeq500.

Which setting would you recommend for quality trimming, as...
Forum: Bioinformatics 05-14-2015, 01:58 AM
Replies: 1
Views: 639
Posted By IonTom
Trimming RNAseq data

When looking at our data the first 10 to 12 bases look strange i FASTQC both for baseq qaulity and composition. This is well known for RNAseq data.

The question now is should I just trim them and...
Forum: Bioinformatics 05-14-2015, 01:53 AM
Replies: 218
Views: 133,381
Posted By IonTom
Dear Alex, i started to use STAR and am...

Dear Alex,

i started to use STAR and am really happy with it.

There are just a few questions:

1. We have different settings. In one we have 150 bases single end reads
in the other 75...
Forum: Bioinformatics 01-29-2015, 04:02 AM
Replies: 1
Views: 876
Posted By IonTom
Best forget about bwa and replace by bwa-mem. ...

Best forget about bwa and replace by bwa-mem.
Thus you have just one step rather than aln ans samse

You can pipe from bwa-me drectly into samtools view to transfrom the sam output into a bam.
...
Forum: Bioinformatics 11-14-2014, 02:32 AM
Replies: 5
Views: 1,678
Posted By IonTom
Have you thought about using Platypus for the...

Have you thought about using Platypus for the task instead of Haplotype caller:
http://www.well.ox.ac.uk/platypus

Both are haplotype based callers but Platypus is multiple times faster.
Forum: Ion Torrent 08-19-2014, 02:58 AM
Replies: 6
Views: 4,257
Posted By IonTom
I don know if the original BWA works Ion Torrent...

I don know if the original BWA works Ion Torrent data. I am currently using BWA-Mem and it works fine. Is there a methylation mapper based on Mem ?

There is also NextGenmap which works well for...
Forum: Bioinformatics 07-07-2014, 09:33 AM
Replies: 6
Views: 5,641
Posted By IonTom
Here is the code: library(gmapR) ...

Here is the code:

library(gmapR)
library(VariantTools)
library(VariantAnnotation)
library(BiocParallel)

biocParam <- MulticoreParam(workers = ncores)

fastaFile <-...
Forum: Bioinformatics 07-07-2014, 09:22 AM
Replies: 6
Views: 5,641
Posted By IonTom
You can use the VariantTools Biocondctor package,...

You can use the VariantTools Biocondctor package, this gives you the
number of unique in read positions for variant and reference. Using a GenomicRanges object generated from a vcf you can make it...
Forum: Bioinformatics 06-25-2014, 05:17 AM
Replies: 0
Views: 732
Posted By IonTom
predictCoding VariantAnnotation TP53 bug

I am trying to annotate some SNPs using the predictCoding function from the VariantAnnotation Bioconductor package. But for some reason it does not annotate some of my SNPs, for the other ones it...
Forum: Ion Torrent 06-18-2014, 12:31 AM
Replies: 9
Views: 9,121
Posted By IonTom
One explanation might come from TMAP. It...

One explanation might come from TMAP.
It basically combines 4 or 5 aligners. Maybe some reads were aligned by another aligner ?
Is the read length the same in all cases ?
Forum: Ion Torrent 06-06-2014, 08:28 AM
Replies: 10
Views: 10,095
Posted By IonTom
What is you application ? Are you doing...

What is you application ?
Are you doing amplicon sequencing of humans ?
More cohorts or single samples ?

You could use another alignement algorithm lile BWA-MEM, Nextgenmap,GEM or Mosaik.
All...
Forum: Ion Torrent 06-06-2014, 08:13 AM
Replies: 9
Views: 9,121
Posted By IonTom
Seems like it is behaving like Ion Torrent data...

Seems like it is behaving like Ion Torrent data normally does.
At least from my experience the homopolymer problem is kind of hard to
fix. Normally you would expect something more stochastic, like...
Forum: Bioinformatics 05-19-2014, 03:58 AM
Replies: 2
Views: 1,560
Posted By IonTom
One of the problems with PGM data and CNVs is...

One of the problems with PGM data and CNVs is that you only analyse amplicons, so coverage over a larger region is not available. Sometimes you also have no access to nomal tissue. One solution i'm...
Forum: Ion Torrent 05-17-2014, 11:43 PM
Replies: 3
Views: 3,798
Posted By IonTom
It should also be noted that Ion Torrent produces...

It should also be noted that Ion Torrent produces a relatively large range of different
read lenghts i.e 30-330.
Forum: Bioinformatics 05-13-2014, 03:06 PM
Replies: 5
Views: 1,939
Posted By IonTom
Here is a solution to the problem above using...

Here is a solution to the problem above using pipes in python

bam_input = "input.bam"
bam_output = "output.bam"

outputter = open(bam_output,mode = "w")

p1 =...
Forum: Ion Torrent 05-10-2014, 08:16 AM
Replies: 3
Views: 3,798
Posted By IonTom
The reads are actually much longer. If you open...

The reads are actually much longer. If you open your aligned BAM/SAM in IGV and make soft clipping visible you should see it. Sometimes you even see things like 235S17M.

In a recent paper they...
Forum: Bioinformatics 05-05-2014, 01:03 PM
Replies: 5
Views: 1,939
Posted By IonTom
Sorry forgot tom post this. Here is the error...

Sorry forgot tom post this.
Here is the error message:

samtools.view("/dev/stdin",_in = bam_IO2)

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File...
Forum: Bioinformatics 05-05-2014, 11:46 AM
Replies: 5
Views: 1,939
Posted By IonTom
Python samtools BytesIO

I currently have a a problem with samtools and python.
Iḿ trying to write a sam or bam file into a file like object
which works well using the following code

import sh
import io

#define...
Forum: Bioinformatics 04-28-2014, 04:29 AM
Replies: 1
Views: 984
Posted By IonTom
Allele Bias

What would you consider the lowest reasonable Allele frequency for a heterozygous germline SNP. Something like between 30% and 60% ?

Also for somatic mutations what would be the limit to a call it...
Forum: Ion Torrent 04-28-2014, 04:25 AM
Replies: 2
Views: 2,948
Posted By IonTom
Calling Indels

What do you think, is it possible to reliably call Indels using the Ion Torrent technology ?

From what i see in the data it seems more or less impossible.
Also quite a few people seem to share...
Showing results 1 to 25 of 32

 


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