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Forum: Bioinformatics 11-09-2017, 08:01 AM
Replies: 2
Views: 547
Posted By Thias
Tons of own, collaborators' and third-party data...

Tons of own, collaborators' and third-party data still aligned to mm9.


So I conclude, that an Ensembl. vs. RefseqGene comparison of the mm10 would approximately have the same result? I didn't...
Forum: Bioinformatics 11-07-2017, 05:52 AM
Replies: 2
Views: 547
Posted By Thias
RefseqGene vs Ensembl for mm9

Hello,

I would like to ask for your opinion regarding a reference transcriptome for mm9. My task is to search for "novel" transcripts in RNA-seq data aligned to mm9, so I am wondering what would...
Forum: Bioinformatics 08-12-2016, 02:10 AM
Replies: 6
Views: 2,916
Posted By Thias
I unfortunately can't give you a ready-to-use...

I unfortunately can't give you a ready-to-use solution, because I never worked with cummeRbund, but I have quite some experience with the underlying ggplot2 and can shed some light on the error...
Forum: Bioinformatics 08-12-2016, 01:37 AM
Replies: 632
Views: 117,403
Posted By Thias
Thanks a lot for your answers! Your exemplified...

Thanks a lot for your answers! Your exemplified replies were really helpful for some more insight.
Forum: Bioinformatics 08-11-2016, 02:28 AM
Replies: 632
Views: 117,403
Posted By Thias
Just because I sometimes stumble over that issue...

Just because I sometimes stumble over that issue in tutorials (which don't seem to bother) and also saw it again in the recent question....

I once was thaugt (and got a deduction of points in a...
Forum: RNA Sequencing 07-22-2016, 02:31 AM
Replies: 0
Views: 822
Posted By Thias
Brainstorming: Error sources for Cuffquant failure: Map Mass: 0.00

Hello folks,

I have an issue with Cuffquant v2.2.1, which fails to quantify the expression (create .cxb files) of the current RNA-seq I am working on:


Inspecting maps and determining...
Forum: Bioinformatics 02-03-2015, 10:44 AM
Replies: 632
Views: 117,403
Posted By Thias
*Sigh*. You know your cardboard homies...

*Sigh*. You know your cardboard homies ("Pappenheimer" (http://www.germany.info/Vertretung/usa/en/__pr/GIC/TWIG__WoW/2011/28-Pappenheimer.html) ;)) too well ...

I was indeed not rebuilding the...
Forum: Bioinformatics 02-03-2015, 07:51 AM
Replies: 632
Views: 117,403
Posted By Thias
Some questions regarding blacklisting

Hello Brian,

Sorry for bothering you again, but I have a question regarding blacklisting and its (correct) usage.

As a favor for a collegue, I quickly mapped some genomic PE data (ChIP-seq) to...
Forum: Bioinformatics 12-09-2014, 02:10 AM
Replies: 632
Views: 117,403
Posted By Thias
Hello Brian, Kudos to you for doing all of...

Hello Brian,

Kudos to you for doing all of that at no time. This will certainly make the bbmap suite even more useful than it already is.

Thanks again
Matthias

BTW: I solved my problem by...
Forum: Bioinformatics 12-07-2014, 07:13 AM
Replies: 632
Views: 117,403
Posted By Thias
Thanks a lot for your kind offer, but your hint...

Thanks a lot for your kind offer, but your hint with the "idtag" is perfectly fine for our purpose, so no need to adjust your code. I just misunderstood the doings of the local=T flag in exactly the...
Forum: Bioinformatics 12-05-2014, 08:01 AM
Replies: 632
Views: 117,403
Posted By Thias
bbmap and multimapper MAPQ

Hello Brian and others,

Usually I run bbmap with the ambig=best parameter and am good to go, but for one of our datasets, it may prove favourable to give multi-mapping reads some special...
Forum: Bioinformatics 06-02-2014, 04:45 AM
Replies: 632
Views: 117,403
Posted By Thias
@GenoMax: Thanks for your answer, but...

@GenoMax: Thanks for your answer, but unfortunately this can't be the problem.

The folder in ref points to an empty directory, because I do not want to include the shRNA sequences to my regular...
Forum: Bioinformatics 06-02-2014, 02:50 AM
Replies: 632
Views: 117,403
Posted By Thias
Hello Brian, I need someone to give me a...

Hello Brian,

I need someone to give me a broad hint. I have already successfully indexed some eukaryotic genomes with BBMAP. But one PhD student in our lab has sequenced a custom shRNA library and...
Forum: Epigenetics 05-19-2014, 05:46 AM
Replies: 1
Views: 1,084
Posted By Thias
As usual, there is not a simple answer. ...

As usual, there is not a simple answer.

Frequently Rollin Hotchkiss (http://www.jbc.org/content/175/1/315.full.pdf) is credited, because he was the first to describe "Epi-cytosine" as a...
Forum: Bioinformatics 05-13-2014, 10:10 AM
Replies: 641
Views: 143,152
Posted By Thias
In case someone else would like to do that on a...

In case someone else would like to do that on a batch of files, this script should help:


#!/bin/bash
find $PWD -type f -name '*.bam' | grep -v "out.bam" | while read SAMPLE
do
...
Forum: Bioinformatics 05-13-2014, 02:53 AM
Replies: 641
Views: 143,152
Posted By Thias
Yes, you have nailed it. The header line for chrX...

Yes, you have nailed it. The header line for chrX is indeed missing in the SAM and it was indeed a multi-FastA which I used as a reference.
Forum: Bioinformatics 05-12-2014, 10:19 AM
Replies: 641
Views: 143,152
Posted By Thias
Hello Bismark-Users, I am a new user of...

Hello Bismark-Users,

I am a new user of Bismark v 0.12.1 and currently familarizing myself with the typical output generated along the pipeline.

Upon a closer look at the .cov and .bedGraph...
Forum: RNA Sequencing 05-09-2014, 03:02 AM
Replies: 3
Views: 2,544
Posted By Thias
Forget what I wrote in the last post (I will not...

Forget what I wrote in the last post (I will not delete it though).

The solution is much simpler. I didn't align the reads myself, but recieved those files from a former collaborator and had no...
Forum: Bioinformatics 04-29-2014, 04:57 AM
Replies: 6
Views: 933
Posted By Thias
Seems your problem is already solved, but in case...

Seems your problem is already solved, but in case you have 5o plot similar data in future again, I recommend the Gviz package on Bioconductor...
Forum: Bioinformatics 04-28-2014, 12:30 AM
Replies: 632
Views: 117,403
Posted By Thias
This in in accordance with my gut feeling, since...

This in in accordance with my gut feeling, since I interpet the Cufflinks docs in the way, that the algorithm adjusts the read weight based on the xmtag:



However Cufflinks in a later stage...
Forum: Bioinformatics 04-26-2014, 01:41 PM
Replies: 632
Views: 117,403
Posted By Thias
Wink Thanks Brian for your response almost at warp...

Thanks Brian for your response almost at warp speed.

Unfortunately am still a bit lost - probably also due to my ignorance regarding the detail SAM Format Specification. This is, how I assumed the...
Forum: Bioinformatics 04-26-2014, 08:32 AM
Replies: 3
Views: 956
Posted By Thias
I have not much experience in running Trinity,...

I have not much experience in running Trinity, but from your logfile it seems that Bowtie existed abnormally and this also caused the Perl wrapper of Trinity to exit. Maybe you should have a closer...
Forum: Bioinformatics 04-26-2014, 08:22 AM
Replies: 632
Views: 117,403
Posted By Thias
@ Brian: Is maxindel the only bbmap parameter you...

@ Brian: Is maxindel the only bbmap parameter you recommend to change for mapping reads for subsequent Cufflinks analysis?

Because I interpetreted the Cufflinks Doc...
Forum: Bioinformatics 03-25-2014, 08:09 AM
Replies: 3
Views: 1,098
Posted By Thias
I know the TargetCaller...

I know the TargetCaller (http://cellnet.cecad.uni-koeln.de/15763.html?&L=0) package for R, but this is mainly for transcription factors. Whether it is suited for Histon ChIP-data you have to test.
Forum: Bioinformatics 03-25-2014, 06:49 AM
Replies: 632
Views: 117,403
Posted By Thias
Yes, I set the threads=8 option and also a memory...

Yes, I set the threads=8 option and also a memory limit of 32g for bbmap.

However I realised that I initially wrote the job script in a way that the scheduler could assign random distributed cores...
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