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Search: Posts Made By: Azazel
Forum: General 06-02-2016, 06:46 PM
Replies: 5
Views: 1,079
Posted By Azazel
Question I want to delete this account, make a new one with my real name, start from scratch

I want to delete this account, Azazel.
I want to make a new account with my real name.
I do not want to change my username. I want to start from scratch.
Is this possible? Cannot find info on how...
Forum: Bioinformatics 02-14-2016, 10:43 PM
Replies: 22
Views: 18,509
Posted By Azazel
This. I do not understand the reasoning behind...

This. I do not understand the reasoning behind blakeoft's suggestion to simply shift everything by 50 into one direction. What is this supposed to achieve? Also, as baritone pointed out the original...
Forum: Sample Prep / Library Generation 09-01-2014, 09:46 PM
Replies: 20
Views: 21,047
Posted By Azazel
Is this published anywhere? Data showing Fragment...

Is this published anywhere? Data showing Fragment Analyzer outperforming Bioanalyzer? If published, would be thankful for a pointer. I'm interested in alternatives to BA as well especially if there...
Forum: The Pipeline 07-05-2014, 07:58 AM
Replies: 5
Views: 9,146
Posted By Azazel
Question Oxford Nanopore MAP: quantitative transcriptomics?

I have the option to join the Oxford Nanopore MAP. What I want to do is use MinION for (quantitative) transcriptomics, i.e. I want to reverse transcribe RNA to DNA and then sequence on MinION. This...
Forum: Bioinformatics 10-24-2013, 09:54 PM
Replies: 0
Views: 2,001
Posted By Azazel
Question exonerate Segmentation Fault on Red Hat Enterprise Linux Server release 6.4

I compiled exonerate-2.2.0 on two different machines:
1) CentOS release 5.8 (Final)
2) Red Hat Enterprise Linux Server release 6.4 (Santiago)

On 1 it works fine, on 2 it crashes immediately with...
Forum: Bioinformatics 10-11-2013, 12:43 AM
Replies: 1
Views: 1,395
Posted By Azazel
Question How can I monitor the progress of BWA?

When aligning a fastq file with BWA, I would like to monitor the progres, to know how long it approx. will take until the alignment of the whole file is finished.

Is there any way to do this?

I...
Forum: Bioinformatics 06-26-2013, 10:40 PM
Replies: 7
Views: 2,242
Posted By Azazel
Now I understand. No, I don't think this is the...

Now I understand. No, I don't think this is the reason because I am not mounting anything external, and the file is definitely there when I use the "file" command, open it in an editor etc.

The...
Forum: Bioinformatics 06-26-2013, 07:34 AM
Replies: 7
Views: 2,242
Posted By Azazel
I am running Xubuntu inside Virtual Box, with...

I am running Xubuntu inside Virtual Box, with Windows 7 as host. Everything is inside VB/Xubuntu, so I don't see how this could affect antyhing.

"file paths local to the VM": sorry, I don not...
Forum: Bioinformatics 06-26-2013, 06:54 AM
Replies: 7
Views: 2,242
Posted By Azazel
These three commands all give me exactly the same...

These three commands all give me exactly the same error message (as described above):

fastaFromBed -name -fi ../rn4/rn4.fa -bed foo.bed -fo bar.fa
getFastaFromBed -name -fi ../rn4/rn4.fa -bed...
Forum: Bioinformatics 06-26-2013, 12:41 AM
Replies: 7
Views: 2,242
Posted By Azazel
Question [bedtools][fastaFrombed] could not stat file

I have a fasta file rn4.fa with the rat genome and also a fai file rn4.fa.fai which I generated with samtools faidx. I want to extract fasta from bed like this (below), but I get an error message...
Forum: Bioinformatics 04-19-2013, 09:05 AM
Replies: 3
Views: 1,292
Posted By Azazel
Thanks for your input Bukowski! I have very...

Thanks for your input Bukowski! I have very similar impressions about these workflow systems.
Forum: Bioinformatics 04-19-2013, 02:07 AM
Replies: 3
Views: 1,292
Posted By Azazel
scientific workflow systems: waste of time or boost of productivity?

I read (online) and hear (conferences) a lot about scientific workflow systems, in the sense of http://en.wikipedia.org/wiki/Scientific_workflow_system.

There are many such systems under...
Forum: Bioinformatics 12-05-2012, 01:49 AM
Replies: 2
Views: 2,830
Posted By Azazel
Question PSL to BED?

How can I convert output from Jim Kent's BLAT, which is in PSL format, into BED format?
Forum: Bioinformatics 12-04-2012, 01:07 AM
Replies: 7
Views: 5,754
Posted By Azazel
@GenoMax: Thanks. I have read the Wikipedia...

@GenoMax: Thanks. I have read the Wikipedia article previously, but I find it ambiguously formulated and I don't know what the "Illumina pipeline" is. As a reader of that article, I know I using...
Forum: Bioinformatics 12-03-2012, 08:08 PM
Replies: 7
Views: 5,754
Posted By Azazel
Question MiSeq fastQ quality scores

I have fastQ files as output from MiSeq, 300bp directional reads. I would like to plot the distribution of quality scores for all bases (using Perl, Gnuplot or R).

I can't find definite...
Forum: Bioinformatics 11-27-2012, 07:51 PM
Replies: 2
Views: 1,101
Posted By Azazel
Hi zhsu, yes you can easily do that. In the UCSC...

Hi zhsu, yes you can easily do that. In the UCSC Genome Browser, just click on "View" at the menu bar at the very top of the page, then "PDF/PS". You probably want then to click on "Download the...
Forum: Bioinformatics 11-26-2012, 09:06 PM
Replies: 2
Views: 1,791
Posted By Azazel
Question noob questions regarding alignment of MiSeq data

I will very soon have results from MiSeq and need to analyze them, in particular do the alignment. The samples have been prepared with a directional RNA-seq protocol, single end. Read length is up to...
Forum: Illumina/Solexa 11-26-2012, 07:24 PM
Replies: 5
Views: 3,546
Posted By Azazel
My experience exactly. First I was excited about...

My experience exactly. First I was excited about BaseSpace, but it is unclear what you can actually do with it and what not, what the pricing structure will be, and most importantly what the security...
Forum: Bioinformatics 09-12-2012, 10:34 PM
Replies: 7
Views: 2,686
Posted By Azazel
Question [cufflinks] every transcript is only one exon

I have a problem with cufflinks, all the transcripts which I assemble always consist of just one exon in the resulting GTF file!

I started with fasta files, aligned them with BLAT. Converted the...
Forum: Bioinformatics 09-09-2012, 04:41 PM
Replies: 1
Views: 4,998
Posted By Azazel
Question [DESeq] baseMean

I would like to ask how exacly baseMean is calculated in DESeq.

According to the manual from 2012-07-24 (http://tinyurl.com/8krvbny) the meaning of the three baseMean columns is:



I...
Forum: Bioinformatics 07-06-2012, 12:52 AM
Replies: 6
Views: 2,270
Posted By Azazel
Question Most straightforward way to prepare input files for PhyloCSF (rat rn4)?

Core question: I did a de novo transcriptome assembly with cufflinks for rat based on RNA-Seq data. There are a couple of 1000 transcripts not overlapping with annotated genes and I would like to...
Forum: Bioinformatics 04-25-2012, 03:26 AM
Replies: 7
Views: 8,659
Posted By Azazel
Thanks sdriscoll for these references, especially...

Thanks sdriscoll for these references, especially the Bullard paper
Forum: Bioinformatics 04-23-2012, 09:14 PM
Replies: 7
Views: 8,659
Posted By Azazel
Just bumping my own thread - would be happy if...

Just bumping my own thread - would be happy if someone could comment or share their thoughts on this issue. Thanks!
Forum: Bioinformatics 04-18-2012, 09:05 PM
Replies: 7
Views: 8,659
Posted By Azazel
Question DESeq: estimateSizeFactors, library size estimation

I am working with high-throuput sequencing data and use DEseq to search for diff. exp. genes.
The protocol is somewhat similar to RNA-Seq, but not exactly RNA-Seq (we are doing a custom paired end...
Forum: General 02-07-2012, 02:11 AM
Replies: 1
Views: 2,599
Posted By Azazel
Anyone ever attended NEB Molecular Biology Summer Workshop or similar?

I am a postdoc doing 100% computational biology in a big genomics research institute. I have zero hands-on wetlab experience.

More and more I think it would be good if I'd gain some wetlab...
Showing results 1 to 25 of 52

 


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