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Search: Posts Made By: sbrohee
Forum: Bioinformatics 06-08-2018, 02:12 AM
Replies: 2
Views: 2,262
Posted By sbrohee
OK... I just ran into a great tool that seems to...

OK... I just ran into a great tool that seems to do exactly what I wanted. It is called VariantBam (https://github.com/walaj/VariantBam, https://www.ncbi.nlm.nih.gov/pubmed/27153727).

./variant...
Forum: Bioinformatics 06-07-2018, 06:33 AM
Replies: 2
Views: 2,262
Posted By sbrohee
Subsample regions of too high coverage

Hi all,

Do you think there is an efficient way of downsampling only a few regions of a bam files (in my case the regions with a too high coverage).

The idea, would be too randomly remove...
Forum: Epigenetics 10-30-2012, 04:57 AM
Replies: 4
Views: 4,844
Posted By sbrohee
Dear all, My tool, called D-peaks, has just...

Dear all,

My tool, called D-peaks, has just been published in Transcription. (http://www.landesbioscience.com/journals/transcription/article/22457/)I think I can now close the subject.

La...
Forum: Bioinformatics 05-04-2012, 06:15 AM
Replies: 7
Views: 9,892
Posted By sbrohee
This is an old post ... but I cannot resist to...

This is an old post ... but I cannot resist to make a small advertising for my (beta-version) tool that might be of interest to some of you.

So I developped a tool which displays high quality...
Forum: Epigenetics 05-02-2012, 06:00 AM
Replies: 4
Views: 4,844
Posted By sbrohee
Dear all, I just finished the web...

Dear all,

I just finished the web implementation of my small visualization tool for binding profiles.

Interested users can test it on...
Forum: Epigenetics 04-16-2012, 04:48 AM
Replies: 4
Views: 4,844
Posted By sbrohee
Hi Ari, Thanks for your proposition, I'll...

Hi Ari,

Thanks for your proposition, I'll try your tool!

However, as I did not get any answer in the beginning, I decided to implement my own tool myself (very simple, in fact). I don't know if...
Forum: Epigenetics 03-22-2012, 08:07 AM
Replies: 4
Views: 4,844
Posted By sbrohee
visualisation of chip-seq profiles ... seqminer?

Dear chip-seq experts :),

My boss would like to have fancy chip-seq profiles (reads arounds TSS) for ... yesterday!
I am quite new to the chip-seq world and I was already very happy to have...
Forum: SOLiD 10-18-2011, 12:19 AM
Replies: 8
Views: 2,440
Posted By sbrohee
@Pmiguel HI Philip. Many thanks for these...

@Pmiguel

HI Philip. Many thanks for these clear and fast answers. This is very helpful.

@ulz_peter

Thank you for the advice. I will mention them but without entering into details (not the...
Forum: SOLiD 10-17-2011, 04:41 AM
Replies: 8
Views: 2,440
Posted By sbrohee
Questions about ABI principle

Hi all,

Even if I am quite new to sequencing, my boss and I decided to initiate talks about next-gen sequencing in our university so that we could stay updated.

I am preparing a talk where I am...
Forum: Bioinformatics 10-12-2011, 06:12 AM
Replies: 1
Views: 1,507
Posted By sbrohee
tophat in background

Hi all,

When running tophat (opensuse 11.4) on our server, I have to keep the terminal window on my desktop computer open otherwise, tophat quits when it goes to the next step (e.g. from python to...
Forum: Bioinformatics 10-12-2011, 05:29 AM
Replies: 4
Views: 2,250
Posted By sbrohee
Thanks a lot for the hints! I will look at them!

Thanks a lot for the hints! I will look at them!
Forum: Bioinformatics 10-12-2011, 05:28 AM
Replies: 12
Views: 3,712
Posted By sbrohee
Bon... Apparently, the solution of cedance...

Bon...

Apparently, the solution of cedance does work ... and I have a nice BAM output file with the options he proposed. Thanks a lot for your help!
Forum: Bioinformatics 10-04-2011, 10:09 AM
Replies: 12
Views: 3,712
Posted By sbrohee
Thanks for the hint. I'll test that tomorrow...

Thanks for the hint. I'll test that tomorrow morning and tell you what!
Forum: Bioinformatics 10-03-2011, 07:04 AM
Replies: 4
Views: 2,250
Posted By sbrohee
Which peak-finder after bowtie? Chip-seq

Hi all,

Which peak-finder tool would you advice me use after having mapped the sequences on the genome with bowtie --best?

Thank you all.
Forum: Bioinformatics 10-03-2011, 06:03 AM
Replies: 12
Views: 3,712
Posted By sbrohee
... still not working ... If someone has...

... still not working ...

If someone has the least idea ...

Thanks to all of you for the help you gave me!
Forum: Bioinformatics 10-03-2011, 04:11 AM
Replies: 12
Views: 3,712
Posted By sbrohee
1) Number of reads per file a)...

1) Number of reads per file
a) kidney_2runs_1.fastq : 39,266,713
b) kidney_2runs_2.fastq : 27,137,793
c) liver_2runs_1.fastq : 54,856,271
d) liver_2runs_2.fastq : 14,761,931

2) There is no...
Forum: Bioinformatics 10-03-2011, 01:55 AM
Replies: 12
Views: 3,712
Posted By sbrohee
Unfortunately... The algorithm does not find any...

Unfortunately... The algorithm does not find any function with tophat 1.2!

Do anyone has another idea?

Moreover, would some of you be able to advice me a good dataset downloadable from some...
Forum: Bioinformatics 10-02-2011, 01:23 AM
Replies: 12
Views: 3,712
Posted By sbrohee
It's the first thing I'll try when arriving at...

It's the first thing I'll try when arriving at work tomorrow morning! Of course, I'll let you know if I succeeded.

Thanks to you all for your help.

Cheers
Forum: Bioinformatics 09-30-2011, 07:18 AM
Replies: 12
Views: 3,712
Posted By sbrohee
No, I haven't... Thanks for the hint! I'll give a...

No, I haven't... Thanks for the hint! I'll give a try.
Forum: Bioinformatics 09-30-2011, 05:25 AM
Replies: 12
Views: 3,712
Posted By sbrohee
tophat does not find any junction

Dear all,

I am very new to the NGS world and my question might seem stupid.

In order to train using RNA-seq data, I downloaded the datasets coming from the paper by Marioni et al (2008) (see...
Forum: Introductions 09-30-2011, 05:07 AM
Replies: 0
Views: 847
Posted By sbrohee
Hello

Hi everyone,

I am a postdoc working in the University of Brussels in Belgium.

During my (short) carreer, I've mainly been interested in questions far far away from next generation sequencing...
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