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Search: Posts Made By: Bukowski
Forum: Illumina/Solexa 02-11-2019, 04:16 AM
Replies: 2
Views: 137
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, 05:18 AM
Replies: 2
Views: 229
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, 07:50 AM
Replies: 1
Views: 229
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, 02:30 AM
Replies: 8
Views: 1,086
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 It uses Tophat, which was superseded by Tophat2,...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, 08:31 AM
Replies: 3
Views: 551
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, 04:23 AM
Replies: 5
Views: 752
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 01-08-2019, 12:35 AM
Replies: 8
Views: 1,086
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, 05:29 AM
Replies: 8
Views: 1,086
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, 04:28 AM
Replies: 8
Views: 1,086
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, 04:45 AM
Replies: 3
Views: 998
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, 06:50 AM
Replies: 6
Views: 612
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, 06:03 AM
Replies: 6
Views: 612
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, 04:24 AM
Replies: 6
Views: 612
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, 02:12 AM
Replies: 7
Views: 540
Posted By Bukowski
Click on my name, and 'send private message'

Click on my name, and 'send private message'
Forum: Bioinformatics 11-21-2018, 01:17 AM
Replies: 7
Views: 540
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, 04:31 AM
Replies: 7
Views: 540
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, 04:39 AM
Replies: 2
Views: 436
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, 04:24 AM
Replies: 1
Views: 403
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, 04:59 AM
Replies: 4
Views: 561
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...
Forum: Bioinformatics 08-20-2018, 04:21 AM
Replies: 4
Views: 561
Posted By Bukowski
Your file name is too long. Shorten it? Where is...

Your file name is too long. Shorten it? Where is that underscore based hell being derived from? If it's coming from the temporary data directory creation try specify a tempdir at execution
Forum: Illumina/Solexa 07-25-2018, 04:13 AM
Replies: 14
Views: 1,129
Posted By Bukowski
What's your %PhiX?

What's your %PhiX?
Forum: RNA Sequencing 07-05-2018, 04:24 AM
Replies: 2
Views: 849
Posted By Bukowski
What do you mean by 'opposite'?

What do you mean by 'opposite'?
Forum: Ion Torrent 06-15-2018, 03:10 PM
Replies: 3
Views: 1,710
Posted By Bukowski
"Accuracy Accurate down to 384-well plates" ...

"Accuracy Accurate down to 384-well plates"

This is a new measure of accuracy that I was previously unaware of.

Their only 'Sequencing Application' in their protocol library is for 16S. There...
Forum: Bioinformatics 06-14-2018, 06:28 AM
Replies: 3
Views: 572
Posted By Bukowski
Some minION sequencing? There's nothing...

Some minION sequencing?

There's nothing wrong with that number of contigs from a 2x250 MiSeq run.
Forum: Bioinformatics 06-14-2018, 02:20 AM
Replies: 3
Views: 572
Posted By Bukowski
Yes, because it acts as an optimiser for Spades.....

Yes, because it acts as an optimiser for Spades.. which is perfectly happy with just short read data.
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