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Forum: General 09-11-2019, 04:52 AM
Replies: 2
Views: 537
Posted By sklages
cross-posted in...

cross-posted in https://www.reddit.com/r/Python/comments/d2ad6l/does_anyone_know_how_to_solve_these_issues/ :rolleyes:
Forum: Pacific Biosciences 08-29-2019, 04:36 AM
Replies: 4
Views: 784
Posted By sklages
Have you already contacted PacBio's techsupport?...

Have you already contacted PacBio's techsupport? They are usually very helpful.
Forum: Bioinformatics 08-29-2019, 04:30 AM
Replies: 19
Views: 8,881
Posted By sklages
Man, this thread is 8 years old .. :)

Man, this thread is 8 years old .. :)
Forum: Bioinformatics 07-30-2019, 05:35 AM
Replies: 1
Views: 512
Posted By sklages
Maybe you find the solution here: ...

Maybe you find the solution here:
https://www.biostars.org/p/387127/
Forum: RNA Sequencing 04-04-2019, 09:17 PM
Replies: 4
Views: 1,290
Posted By sklages
Looks like your genome generation failed. There...

Looks like your genome generation failed. There are missing quite a few files.

Have a look at Are you seeing some errors?
Usually it should finish with sth. like:


And yes, just to be sure,...
Forum: Illumina/Solexa 12-05-2018, 04:35 AM
Replies: 2
Views: 1,568
Posted By sklages
Why would I want to access the machine itself? We...

Why would I want to access the machine itself? We connected a very fast fileserver running linux and a samba... This server i mapped on the NextSeq. BCL conversion grabs the data from the file server...
Forum: Oxford Nanopore 12-05-2018, 04:29 AM
Replies: 5
Views: 2,854
Posted By sklages
That's probably not possible. But you could...

That's probably not possible. But you could connect with sth. TeamViewer [1] to see and also control the PC running MinKnow.


[1] https://www.teamviewer.com
Forum: General 10-23-2018, 04:55 AM
Replies: 0
Views: 1,188
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, 04:47 AM
Replies: 0
Views: 1,565
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, 06:49 AM
Replies: 17
Views: 7,174
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, 05:33 AM
Replies: 17
Views: 7,174
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, 05:17 AM
Replies: 17
Views: 7,174
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, 02:58 AM
Replies: 17
Views: 7,174
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, 02:48 AM
Replies: 0
Views: 579
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, 04:27 AM
Replies: 7
Views: 3,135
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, 09:58 PM
Replies: 7
Views: 3,135
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, 10:31 PM
Replies: 7
Views: 3,135
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, 11:11 AM
Replies: 107
Views: 26,151
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, 10:57 AM
Replies: 3
Views: 5,478
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, 12:06 AM
Replies: 21
Views: 6,370
Posted By sklages
Have a look at...

Have a look at https://downloads.pacbcloud.com/public/SequelData/ArabidopsisDemoData/
Forum: Illumina/Solexa 09-16-2016, 01:21 AM
Replies: 9
Views: 2,597
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, 10:29 PM
Replies: 9
Views: 2,597
Posted By sklages
GenoMax, thanks for the numbers. That makes me...

GenoMax, thanks for the numbers. That makes me optimistic :-)
Forum: Illumina/Solexa 09-14-2016, 11:16 PM
Replies: 9
Views: 2,597
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, 03:36 AM
Replies: 9
Views: 2,597
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, 12:50 AM
Replies: 36
Views: 4,639
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...
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