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Search: Posts Made By: Dolphin22
Forum: General 02-27-2014, 01:21 AM
Replies: 0
Views: 472
Posted By Dolphin22
Database for Arginine Methylation

Hey folks,

I am desperately looking for a database on arginine methylation in plants. I need the information for my research.

If anyone knows a database pls help

Best regards
Forum: General 01-14-2014, 01:56 AM
Replies: 1
Views: 731
Posted By Dolphin22
Import blastp alignments to jalview

Hey folks

what is the best way to import an alignment blastp into jalview? I did not find satisfactory results in the web

thx
Forum: Bioinformatics 09-19-2013, 04:29 AM
Replies: 1
Views: 929
Posted By Dolphin22
Tool for loci localization on chromosomes

Hey everybody.

I am looking for a tool to visualize specific loci on chromosomes structures of Arabidopsis thaliana. The result shoulb something like this.
...
Forum: Bioinformatics 04-22-2013, 07:11 AM
Replies: 0
Views: 483
Posted By Dolphin22
tool to finf 22mer in small RNAseq library

Hey there,

I am looking for a tool to search small RNA Seq libraries for specific 22mers and as an output I need the number of hits for each 22mer

Is there anything out there that can do this?...
Forum: RNA Sequencing 02-08-2013, 01:04 AM
Replies: 1
Views: 2,874
Posted By Dolphin22
experiences ncPRO-seq

Hey everybody

recently I stumbled over ncPRO-seq. A tool for profiling of non-coding RNAs in sRNA-seq data (Publication:PMID: 23044543).

At the moment I cannot reach the mentioned webpage. I...
Forum: Introductions 10-24-2012, 04:07 AM
Replies: 2
Views: 487
Posted By Dolphin22
Hey good to know. What are doing in your...

Hey

good to know. What are doing in your company in detail?
Forum: Helicos / Direct Genomics 10-24-2012, 04:00 AM
Replies: 1
Views: 2,768
Posted By Dolphin22
Download of example Data Helicos

Hey folks

I am looking for example Helicos data to test my algorithms. Does anyone know any repository where I can download such data? Are they already on GEO?
Forum: Bioinformatics 10-03-2012, 07:36 AM
Replies: 4
Views: 754
Posted By Dolphin22
Yes I know but I can only load the bam file into...

Yes I know but I can only load the bam file into tablet and not the index file
Forum: Bioinformatics 10-03-2012, 07:30 AM
Replies: 4
Views: 754
Posted By Dolphin22
indexed bam file

What is exactly an indexed bam file?
I already have a bam file AND a bai file. Is this already an indexed bam file? I could successfully load it into IGV but did not manage to do with Tablet
Forum: Bioinformatics 10-03-2012, 07:27 AM
Replies: 122
Views: 36,581
Posted By Dolphin22
Hey I have a bit of a problem. I already...

Hey

I have a bit of a problem. I already have a bam file and a fai file. How do I load the bam AND the bai file into tablet to have all features?
I just managed to load the bam file without any...
Forum: Bioinformatics 10-01-2012, 07:28 AM
Replies: 2
Views: 1,395
Posted By Dolphin22
Visualization of sam file to find introns

Hey guys

I have a .sam file from bowtie2 and I want to see if there is a high number of reads mapped on intronic sequences..
What is the fastest solution? I planned to visualize the alignment...
Forum: Service Providers 10-01-2012, 01:31 AM
Replies: 162
Views: 126,929
Posted By Dolphin22
Hi the University of Veterinary Medicine...

Hi

the University of Veterinary Medicine Vienna does not offer sequencing service anymore.
The DKFZ only for internal personal and the University of Edinburgh only for the UK market.
Forum: Bioinformatics 10-01-2012, 01:27 AM
Replies: 5
Views: 1,755
Posted By Dolphin22
Hi there, you could also use Integrated...

Hi there,

you could also use Integrated Genome Browser
http://bioviz.org/igb/
Forum: Illumina/Solexa 10-01-2012, 12:43 AM
Replies: 2
Views: 79,146
Posted By Dolphin22
Multiplexing vs single plexing

Hey guys

I have a question on multiplexing libraries:

1) When is it useful to do multiplexing and when should you do one library per lane?

2) What are the advantages/disadvantages of...
Forum: Illumina/Solexa 09-27-2012, 07:20 AM
Replies: 3
Views: 997
Posted By Dolphin22
Where perform Illumina totalRNAseq?

Hey guys

I am planning to do totalRNASeq studies using Illumina. Do you have any suggestions where to perform the sequencing? Do you know any companies or academic genome centers preferably in...
Forum: Literature Watch 09-26-2012, 12:05 AM
Replies: 2
Views: 1,357
Posted By Dolphin22
Could be quite interesting to read. But...

Could be quite interesting to read. But unfortunately I cannot get the pdf file from my University. Perhaps somebody of you can help me out?
Forum: Helicos / Direct Genomics 09-19-2012, 06:10 AM
Replies: 18
Views: 8,606
Posted By Dolphin22
Thanks for your reply. I did use the...

Thanks for your reply.
I did use the Helipshere software for the analyis so the artifacts should be removed automatically. But I will check the nucleotide distribution of my unaligned sequences...
Forum: Helicos / Direct Genomics 09-17-2012, 10:11 AM
Replies: 18
Views: 8,606
Posted By Dolphin22
@ singlemoleculer Thanks for your advices. I...

@ singlemoleculer
Thanks for your advices. I checked my sequences but I am not sure about some points:

What does very rich of A's and T's mean? Do you have a percentage? The same with the low...
Forum: RNA Sequencing 08-23-2012, 11:56 PM
Replies: 1
Views: 1,411
Posted By Dolphin22
Formaldehyde fixation and RNA Seq - possible?

Hey there

We have done Helicos Sequencing of Arabaidopsis RNA. The tissues were crosslinked with formaldehyde and the FA was washed away before putting into the sequencer. Analysis revealed that...
Forum: Introductions 07-16-2012, 05:40 AM
Replies: 0
Views: 438
Posted By Dolphin22
Hello everybody

I am mainly working with RNA-Sequencing methods to analyze miRNAs (Illumina) but we also used Helicos technology to run total RNA analysis. Basically I come from wet lab and started about 8 month ago...
Forum: General 07-16-2012, 05:03 AM
Replies: 1
Views: 799
Posted By Dolphin22
Tool for short nucleotide sequences

Hey there,

I am not sure where to put that so I opened a thread here.
I have a bunch of short nucleotide sequences (21 nts). My goal is to align these sequences to all introns of the TAIR10...
Forum: Bioinformatics 07-04-2012, 07:36 AM
Replies: 4
Views: 1,443
Posted By Dolphin22
@chadn737 Sounds good thanks for the advice!! ...

@chadn737 Sounds good thanks for the advice!!

Do you a source where I can download a binary fo HTSeq for Windows? I was looking at http://pypi.python.org/pypi/HTSeq but I could not find a binary....
Forum: Bioinformatics 07-04-2012, 04:23 AM
Replies: 4
Views: 1,443
Posted By Dolphin22
Genome Browser to visualize RNA-Seq Data

Hey there,

I am looking for a Genome Browser that is able to visualize my Helicos sequencing data (BAM-files) on the Arabidopsis transcriptome (TAIR10) and additionally having the possibility to...
Forum: Helicos / Direct Genomics 07-04-2012, 04:15 AM
Replies: 18
Views: 8,606
Posted By Dolphin22
Hey everybody, good to have some people...

Hey everybody,

good to have some people already having some experience with Helicos.

In our Lab we are working on an RNA binding protein and try to figure out putative target RNAs. Therefore we...
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