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Search: Posts Made By: Bukowski
Forum: Pacific Biosciences Yesterday, 05:12 AM
Replies: 4
Views: 149
Posted By Bukowski
One of them is an optical platform doing laser...

One of them is an optical platform doing laser based detection of nanometre scale wells, and the other ... isn't. You can't 'skip the details' here, the details are the reason ;)
Forum: RNA Sequencing 03-15-2019, 04:28 AM
Replies: 1
Views: 152
Posted By Bukowski
I wouldn't have thought so. You require all the...

I wouldn't have thought so. You require all the reads to assemble the genome, so splitting this across a cluster, without a shared/distributed memory model, doesn't fit the assembly paradigm which is...
Forum: Illumina/Solexa 03-13-2019, 04:19 AM
Replies: 3
Views: 169
Posted By Bukowski
short answer: yes

short answer: yes
Forum: Illumina/Solexa 03-07-2019, 03:26 AM
Replies: 3
Views: 255
Posted By Bukowski
It kind of sounds like your sequencing provider...

It kind of sounds like your sequencing provider hasn't bothered to demux on the dual index.

You might be able to use bbtools Demuxbyname.sh

http://seqanswers.com/forums/showthread.php?t=58221
...
Forum: RNA Sequencing 02-27-2019, 05:33 AM
Replies: 2
Views: 323
Posted By Bukowski
I don't think they say it's only good for...

I don't think they say it's only good for eukaryotes, just that it mimics the nature of eukaryotic transcripts in terms of nucleotide content, size distribution, polyadenylation etc. I think the...
Forum: Illumina/Solexa 02-19-2019, 03:53 AM
Replies: 4
Views: 312
Posted By Bukowski
Not necessarily, the clustering of the flowcells...

Not necessarily, the clustering of the flowcells is completely different on a NovaSeq to a MiSeq - so if they think the pool is balanced on the MiSeq, I'd certainly be looking at the size...
Forum: Illumina/Solexa 02-11-2019, 03:16 AM
Replies: 2
Views: 333
Posted By Bukowski
Maybe. There is not enough data here to answer...

Maybe. There is not enough data here to answer the question. How did you determine the expected genome size? What is the variation in known genome sizes?

Have a look at:
...
Forum: Illumina/Solexa 02-06-2019, 04:18 AM
Replies: 2
Views: 429
Posted By Bukowski
I think you'll find this has been answered...

I think you'll find this has been answered before:

http://seqanswers.com/forums/showthread.php?t=75899
Forum: Bioinformatics 01-30-2019, 06:50 AM
Replies: 1
Views: 307
Posted By Bukowski
People who don't understand the value of a...

People who don't understand the value of a bioinformatician.
Forum: RNA Sequencing 01-21-2019, 01:30 AM
Replies: 8
Views: 1,287
Posted By Bukowski
I just looked at the GenePattern workflow. I can...

I just looked at the GenePattern workflow. I can think of a number of reasons why this might be happening still, but this workflow is EXTREMELY dated. It uses Tophat, which was superseded by Tophat2,...
Forum: Core Facilities 01-19-2019, 07:31 AM
Replies: 3
Views: 829
Posted By Bukowski
Of course you can submit cDNA for sequencing, at...

Of course you can submit cDNA for sequencing, at this point it's just 'DNA'. Most cores would probably prefer to take the RNA because then the library preparation is in their hands, and not yours -...
Forum: Pacific Biosciences 01-08-2019, 03:23 AM
Replies: 5
Views: 940
Posted By Bukowski
Judging from the total size of the contigs that...

Judging from the total size of the contigs that would be my suspicion, because it looks like you have the whole 5.5Mb there in some form - just not in a single contig (which you can't guarantee, even...
Forum: RNA Sequencing 01-07-2019, 11:35 PM
Replies: 8
Views: 1,287
Posted By Bukowski
IGV would be fine - I'm just interested in...

IGV would be fine - I'm just interested in whether there are any reads mapping to that region
Forum: RNA Sequencing 01-07-2019, 04:29 AM
Replies: 8
Views: 1,287
Posted By Bukowski
So have you visualised the read aligments in the...

So have you visualised the read aligments in the region in the patients?
Forum: RNA Sequencing 01-07-2019, 03:28 AM
Replies: 8
Views: 1,287
Posted By Bukowski
Far too many reasons to possibly speculate on...

Far too many reasons to possibly speculate on from incorrectly running the analysis, to low read coverage in your patient samples to QC differences between the samples to differences is sample...
Forum: 454 Pyrosequencing 12-19-2018, 03:45 AM
Replies: 3
Views: 1,149
Posted By Bukowski
QIAGEN bought Biotage (what was Pyrosequencing AB...

QIAGEN bought Biotage (what was Pyrosequencing AB and the original outlicencing entity for the IP) in 2008. The PyroMark assays have been available from QIAGEN for about that length of time from...
Forum: Bioinformatics 11-28-2018, 05:50 AM
Replies: 6
Views: 677
Posted By Bukowski
You can crudely combine fastq.gz files with the...

You can crudely combine fastq.gz files with the 'cat' command, you just need to concatenate the 'forward' and 'reverse' reads for each sample separately

cat fastq_sample1_lane1_R1.fastq.gz...
Forum: Bioinformatics 11-28-2018, 05:03 AM
Replies: 6
Views: 677
Posted By Bukowski
Well at least you have replicates, that is a good...

Well at least you have replicates, that is a good start. But your 'forward' and 'reverse' reads are not different samples - and your maths doesn't stack.

4 treatments x 5 replicates = 20 samples....
Forum: Bioinformatics 11-28-2018, 03:24 AM
Replies: 6
Views: 677
Posted By Bukowski
What's the question? HISAT replaces TopHat...

What's the question?

HISAT replaces TopHat anyway, so no point running them both. If you want to try something different try Kallisto/sleuth or other pseudoalignment approach.

Questions not to...
Forum: Bioinformatics 11-21-2018, 01:12 AM
Replies: 7
Views: 571
Posted By Bukowski
Click on my name, and 'send private message'

Click on my name, and 'send private message'
Forum: Bioinformatics 11-21-2018, 12:17 AM
Replies: 7
Views: 571
Posted By Bukowski
Why don't you drop me a private message?

Why don't you drop me a private message?
Forum: Bioinformatics 11-20-2018, 03:31 AM
Replies: 7
Views: 571
Posted By Bukowski
I am pretty sure that accounts are manually added...

I am pretty sure that accounts are manually added there, I got my login eventually but it was no means instantaneous.
Forum: Bioinformatics 11-16-2018, 03:39 AM
Replies: 2
Views: 464
Posted By Bukowski
What are you mapping the contigs back to the...

What are you mapping the contigs back to the reference with?

You could perhaps try reordering the contigs with progressive Mauve against the 'reference' genome, which might not be that good a...
Forum: Bioinformatics 10-19-2018, 03:24 AM
Replies: 1
Views: 418
Posted By Bukowski
Chances are the overlap isn't enough with the...

Chances are the overlap isn't enough with the quality of the 600 cycle kits and any quality trimming in a pipeline, the normal recommendation is just to use the F reads as these are higher quality.
Forum: Bioinformatics 08-20-2018, 03:59 AM
Replies: 4
Views: 593
Posted By Bukowski
Are you running under a job scheduler? I just...

Are you running under a job scheduler? I just tried to run the tests, but merman doesn't seem to compile under g++ 5.5.0 - and in fact there's an open issue on that repo that's 3.5 years old, which...
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