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Forum: General 10-23-2018, 05:55 AM
Replies: 0
Views: 258
Posted By sklages
What happened to http://omicsmaps.com/ ?

Just wanted to have a look at http://omicsmaps.com/ but the site is dead. I haven't checked for some time, but has this project been discontinued?
Forum: General 02-15-2018, 05:47 AM
Replies: 0
Views: 1,253
Posted By sklages
Bgiseq-500

The only info available for BGISEQ-500 can be found here,
http://www.seq500.com/en/

Has anyone any insights, numbers, release date or something that can shed a bit more light on that machine?
Forum: Pacific Biosciences 09-07-2017, 07:49 AM
Replies: 14
Views: 4,189
Posted By sklages
It's probably a good idea to adjust the quality...

It's probably a good idea to adjust the quality dummy values to something "more or less good", e.g. 30 or more before using third-party tools ..
Forum: Pacific Biosciences 09-07-2017, 06:33 AM
Replies: 14
Views: 4,189
Posted By sklages
That what my first thought too ... it is not a...

That what my first thought too ... it is not a very smart idea choosing basically a "junk value" :-)
Forum: Pacific Biosciences 09-07-2017, 06:17 AM
Replies: 14
Views: 4,189
Posted By sklages
Which BAM are you reading? "subreads"? PacBio...

Which BAM are you reading? "subreads"? PacBio stated back in february:

"The subread-bam/fastq files do not have quality values associated to the bases. In fact none of our SMRT Analysis tools use...
Forum: Pacific Biosciences 09-07-2017, 03:58 AM
Replies: 14
Views: 4,189
Posted By sklages
What platform? At least for Sequel data the...

What platform? At least for Sequel data the subread-bam/fastq files do not have quality values associated to the bases. So there is a dummy value for each base, zero, "!".
Forum: Bioinformatics 06-14-2017, 03:48 AM
Replies: 0
Views: 453
Posted By sklages
UCSC Genome Browser Alternative?

Hi Folks,

for some reasons we'd like to get rid of UCSC GB and use some other software to (locally) provide mammalian-sized genome data and annotation for remote access via web browser or other...
Forum: Bioinformatics 06-02-2017, 05:27 AM
Replies: 7
Views: 2,263
Posted By sklages
After studying some docs I do see that with...

After studying some docs I do see that with optional MD:Z I am even as flexible as with X=, with the advantage of not having too "complicated" CIGARs. :-)
Forum: Bioinformatics 06-01-2017, 10:58 PM
Replies: 7
Views: 2,263
Posted By sklages
Brian, thanks for the suggestion. I will try...

Brian,

thanks for the suggestion. I will try :-)

Nevertheless I'd wish bwa would provide an option to either use M or X=.
Just to avoid more I/O due to another conversion ...

Sven
Forum: Bioinformatics 05-30-2017, 11:31 PM
Replies: 7
Views: 2,263
Posted By sklages
Are there any plans to extend bwa to write X/=...

Are there any plans to extend bwa to write X/= instead of M? At least optional?
Forum: Bioinformatics 12-14-2016, 12:11 PM
Replies: 90
Views: 15,991
Posted By sklages
Interesting tool. Though I'd wish it could deal...

Interesting tool. Though I'd wish it could deal with "twin files", as these are the initial "raw files" of Illumina's bcl2fastq output. Additionally many tools require the pairs to be separated ......
Forum: De novo discovery 12-14-2016, 11:57 AM
Replies: 3
Views: 3,865
Posted By sklages
Please do not crosspost to Biostars if you want...

Please do not crosspost to Biostars if you want help here ..

jellyfish is in your PATH, runCA is not.

You could either use --path /PATH/TO/runCA with masurca or add the corresponding path to...
Forum: Pacific Biosciences 11-16-2016, 01:06 AM
Replies: 21
Views: 5,481
Posted By sklages
Have a look at...

Have a look at https://downloads.pacbcloud.com/public/SequelData/ArabidopsisDemoData/
Forum: Illumina/Solexa 09-16-2016, 02:21 AM
Replies: 9
Views: 1,989
Posted By sklages
That's what I was interested in :-) But btw,...

That's what I was interested in :-)

But btw, what's the fastq output for such runs (roughly)?
Forum: Illumina/Solexa 09-15-2016, 11:29 PM
Replies: 9
Views: 1,989
Posted By sklages
GenoMax, thanks for the numbers. That makes me...

GenoMax, thanks for the numbers. That makes me optimistic :-)
Forum: Illumina/Solexa 09-15-2016, 12:16 AM
Replies: 9
Views: 1,989
Posted By sklages
Sure. For our HiSeq 2000 a few years ago, we had...

Sure. For our HiSeq 2000 a few years ago, we had folder sizes up to 4TB; Illumina stated in their FAQ that a run folder is roughly 1TB.

I am just curious how real-world numbers align with...
Forum: Illumina/Solexa 09-14-2016, 04:36 AM
Replies: 9
Views: 1,989
Posted By sklages
Smile HiSeq 4000 : typical RAW data output in GBytes

Hi,

can someone provide some info on how much raw data (in terms of GBytes, not Gbases) is generated for some typical HiSeq 4000 WGS runs (150,75, whatever)? How much fastq data (GBytes) is...
Forum: Bioinformatics 08-29-2016, 01:50 AM
Replies: 36
Views: 3,508
Posted By sklages
Hallo again ;-) we are now with Isaac3. Cool...

Hallo again ;-)

we are now with Isaac3. Cool .. ;-)

Creating indices for grch38 and grcm38 leaves some open questions:

I have run index creation as follows (mask-width 0 is the default, I...
Forum: Illumina/Solexa 08-19-2016, 12:27 AM
Replies: 3
Views: 952
Posted By sklages
oh, I missed the 'pre' :-) So you probably...

oh, I missed the 'pre' :-)

So you probably should ask Illumina directly for their recommendation of processing such data.
Forum: Illumina/Solexa 08-17-2016, 12:08 AM
Replies: 3
Views: 952
Posted By sklages
You may want to try...

You may want to try https://github.com/sequencing/NxTrim .. It is an Illumina tool for mp read processing.
Forum: Open Genomics Engine Project 08-17-2016, 12:03 AM
Replies: 14
Views: 43,184
Posted By sklages
Yepp, .. project development has been...

Yepp, .. project development has been discontinued..

Latest news is:
Forum: Metagenomics 07-12-2016, 11:29 PM
Replies: 7
Views: 1,946
Posted By sklages
It would still be interesting, what has caused...

It would still be interesting, what has caused the reads to be out-of-sync.
Have these reads been pre-processed with some tool before or is this the data that has been sent by sequencing provider?
...
Forum: Bioinformatics 06-20-2016, 07:11 AM
Replies: 5
Views: 1,115
Posted By sklages
This might be interesting for you:...

This might be interesting for you: http://www.illumina.com/platinumgenomes/
Forum: Illumina/Solexa 05-24-2016, 07:00 AM
Replies: 12
Views: 3,854
Posted By sklages
Just curious, why do you want to store CIFs on a...

Just curious, why do you want to store CIFs on a NextSeq system?
Forum: Illumina/Solexa 05-10-2016, 03:43 AM
Replies: 18
Views: 6,675
Posted By sklages
Still you need to check how much RAM your 58...

Still you need to check how much RAM your 58 threads consume on your machine.
Check if IO bandwidth is sufficient; are you the only one reading from / writing to the filesystem with your job?
...
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