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Search: Posts Made By: Bukowski
Forum: Bioinformatics 11-28-2018, 06:50 AM
Replies: 6
Views: 406
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: 406
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: 406
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: 411
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: 411
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: 411
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: 349
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: 363
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: 523
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: 523
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: 962
Posted By Bukowski
What's your %PhiX?

What's your %PhiX?
Forum: RNA Sequencing 07-05-2018, 04:24 AM
Replies: 2
Views: 786
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: 1,355
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: 480
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: 480
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.
Forum: Bioinformatics 03-29-2018, 04:20 AM
Replies: 3
Views: 984
Posted By Bukowski
Well - you try pipetting so accurately that you...

Well - you try pipetting so accurately that you can manage better... ;)

Quantification isn't exact. Dilution isn't exact. Pooling isn't exact.
Forum: Bioinformatics 03-23-2018, 05:31 AM
Replies: 6
Views: 1,072
Posted By Bukowski
Use rsync?

Use rsync?
Forum: Illumina/Solexa 02-28-2018, 12:55 PM
Replies: 2
Views: 1,103
Posted By Bukowski
I don't really know what your application is, but...

I don't really know what your application is, but leaving yourself only 5 bp overlap for the reads at 2x75 doesn't sound like its the ideal strategy for flashing reads. How much fidelity do you need...
Forum: Bioinformatics 02-10-2018, 04:42 PM
Replies: 3
Views: 820
Posted By Bukowski
It's down. https://gitlab.com/ezlab/busco ...

It's down.

https://gitlab.com/ezlab/busco

You can find links to the code and datasets there.
Forum: Bioinformatics 01-22-2018, 01:58 AM
Replies: 15
Views: 1,340
Posted By Bukowski
What was the goal of sequencing them in the first...

What was the goal of sequencing them in the first place? This might inform any potential answers...
Forum: Ion Torrent 01-17-2018, 04:58 AM
Replies: 5
Views: 2,289
Posted By Bukowski
'Deblur has not been evaluated with Ion Torrent':...

'Deblur has not been evaluated with Ion Torrent': https://forum.qiime2.org/t/deblur-p-trim-length-deactivation-failure/1880/5

DADA2 recommendations for Ion Torrent data:...
Forum: Illumina/Solexa 12-19-2017, 04:44 AM
Replies: 2
Views: 951
Posted By Bukowski
https://support.illumina.com/downloads/sequencing_...

https://support.illumina.com/downloads/sequencing_coverage_calculator.html
Forum: Bioinformatics 11-09-2017, 04:40 AM
Replies: 2
Views: 604
Posted By Bukowski
https://www.biostars.org/p/109425/

https://www.biostars.org/p/109425/
Forum: Academic/Non-Profit Jobs 10-12-2017, 08:58 AM
Replies: 0
Views: 436
Posted By Bukowski
Research Fellow in Microbial Genomics, Aberdeen - Sctoland

Posting on behalf of a colleague:

REF: SBS028R

We seek a highly motivated and interactive Microbial Genomicist to take a leading role in a Natural Environment Research Council-funded project...
Forum: Academic/Non-Profit Jobs 08-07-2017, 02:34 AM
Replies: 0
Views: 427
Posted By Bukowski
Genomics Pipeline Group Software Developer - Earlham Institute, Norwich UK

We currently have a job open in the Genomics Pipelines Group for a Software Developer. Please note this is not a bioinformatics post per se, but will work closely with bioinformaticians and others in...
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