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Forum: Academic/Non-Profit Jobs 10-14-2019, 05:14 AM
Replies: 0
Views: 264
Posted By colindaven
Hannover, Gemany. PhD position in translational implementation of metagenomics

PhD position in translational clinical implementation of metagenomics

A PhD position is available for 3 years in the Research Core Unit Genomics at Hannover Medical School in Hannover, Germany...
Forum: General 09-12-2019, 07:57 AM
Replies: 1
Views: 740
Posted By colindaven
You don't mention any bioinformatics processes...

You don't mention any bioinformatics processes used, so it is impossible to answer your question.

What you mean is during the read mapping pipeline (FASTQ-> BAM).

We use NextSeq frequently and...
Forum: Bioinformatics 07-31-2019, 04:51 AM
Replies: 8
Views: 1,200
Posted By colindaven
Freebayes, the SNV caller, is another heavily...

Freebayes, the SNV caller, is another heavily used tool with just a preprint.

From the github site:
"
A preprint Haplotype-based variant detection from short-read sequencing provides an overview...
Forum: Academic/Non-Profit Jobs 07-11-2019, 07:33 AM
Replies: 0
Views: 401
Posted By colindaven
PhD position in translational clinical implementation of metagenomics

A PhD position is available for 3 years in the Research Core Unit Genomics at Hannover Medical School in Hannover, Germany starting in October 2019 (or later). Salary will be according to the...
Forum: Academic/Non-Profit Jobs 07-11-2019, 07:24 AM
Replies: 0
Views: 312
Posted By colindaven
Bioinformatics PhD position in Next Generation Sequencing analysis

A Bioinformatics PhD position is available for 3 years in the group of Burkhard Tümmler at Hannover Medical School in Hannover, Germany starting in October 2019 (or later). Salary will be according...
Forum: SOLiD 07-11-2019, 06:38 AM
Replies: 1
Views: 1,868
Posted By colindaven
Well, the main thing is your csfasta and qual...

Well, the main thing is your csfasta and qual files work fine.

Could BC be barcode ? They seemt to be short, as in barcodes, and the format seems to be the csfasta format.

Not sure I ever saw...
Forum: Bioinformatics 07-01-2019, 04:52 AM
Replies: 2
Views: 371
Posted By colindaven
The error says it all "could not find...

The error says it all "could not find bedGraphToBigWig".

Have a read about Linux and PATH and and or install/configure this program properly in your PATH.

Else try deeptools via bioconda, it's...
Forum: Bioinformatics 05-21-2019, 06:55 AM
Replies: 2
Views: 561
Posted By colindaven
Why not use the scaffolds ? These are the final...

Why not use the scaffolds ? These are the final contigs organised into scaffolds by using the supplied probably mate pair info. This is what I have always used.

If you still want the contigs,...
Forum: Bioinformatics 05-21-2019, 05:44 AM
Replies: 2
Views: 716
Posted By colindaven
Why not just specify -nanopore-corrected to...

Why not just specify -nanopore-corrected to probably make canu skip this stage ?

Also, why would you even want to do this ? You'll get really awful results, the correction is there for a reason.
...
Forum: Bioinformatics 05-08-2019, 06:58 AM
Replies: 2
Views: 679
Posted By colindaven
You're right, these full VCFs are rare. I think a...

You're right, these full VCFs are rare. I think a lot of the problems are due to data privacy. You can get them from the TCGA archive but that takes a lot of time to gain access.

I don't do a lot...
Forum: Bioinformatics 05-08-2019, 06:53 AM
Replies: 2
Views: 864
Posted By colindaven
Bit late, but you could do this nmtag=f ...

Bit late, but you could do this

nmtag=f Write NM tags.

and then filter by NM = number of mismatches later.

This might be easier:

editfilter=-1 Ban alignments...
Forum: Bioinformatics 05-08-2019, 06:45 AM
Replies: 1
Views: 606
Posted By colindaven
Hmm. You might want to use the aggregated...

Hmm. You might want to use the aggregated webstores of RNA-seq like recount2 or others.

https://jhubiostatistics.shinyapps.io/recount/

I would combine and put them into a nice web tool like...
Forum: Bioinformatics 01-23-2019, 04:57 AM
Replies: 2
Views: 659
Posted By colindaven
Try using Maker -which includes augustus - and or...

Try using Maker -which includes augustus - and or gmap with a GFF3 output option.
Forum: Bioinformatics 01-09-2019, 05:03 AM
Replies: 1
Views: 899
Posted By colindaven
I think JBrowse desktop is a lot faster, cleaner...

I think JBrowse desktop is a lot faster, cleaner and nicer than those two.

I haven't used IGB for a while, but whatever works for you! IGV is just the most well known standalone genome browser in...
Forum: Bioinformatics 12-11-2018, 07:27 AM
Replies: 6
Views: 1,201
Posted By colindaven
Putty is a bit lame these days. Does...

Putty is a bit lame these days.

Does mobaxterm work on it ?

https://mobaxterm.mobatek.net/
Forum: Bioinformatics 09-13-2018, 04:44 AM
Replies: 2
Views: 785
Posted By colindaven
Diploid assemblers are very new, and are only...

Diploid assemblers are very new, and are only being applied by pioneering groups in the last couple of years. To my knowledge most groups are still doing haploid assemblies, and noone has delved into...
Forum: Bioinformatics 09-13-2018, 04:17 AM
Replies: 2
Views: 783
Posted By colindaven
Muscle might be good. MUGSY is probably excellent...

Muscle might be good. MUGSY is probably excellent for this use case given the length of the sequence.

cheers
Colin
Forum: Oxford Nanopore 05-31-2018, 04:50 AM
Replies: 1
Views: 2,801
Posted By colindaven
Nice work, cheers. For me the most exciting news...

Nice work, cheers. For me the most exciting news has to be the reasonably high output from the Promethion. This has the potential to be a single assay which may yield methylation, de novo assembly,...
Forum: Bioinformatics 05-02-2018, 05:01 AM
Replies: 1
Views: 1,388
Posted By colindaven
STAR or Hisat2, and NOT Tophat2

STAR or Hisat2, and NOT Tophat2
Forum: Bioinformatics 04-16-2018, 07:10 AM
Replies: 13
Views: 2,062
Posted By colindaven
Its' very tricky to analyse 10X pacbio data and...

Its' very tricky to analyse 10X pacbio data and do a de novo assembly. I have had very bad experiences in the past with this setup, getting poor N50s and putting lots of effort in. 30x+ is far, far...
Forum: Bioinformatics 04-16-2018, 07:05 AM
Replies: 2
Views: 1,545
Posted By colindaven
Tricky. Perhaps its not possible. However,...

Tricky. Perhaps its not possible.

However, you can do something similar I believe with deeptools (see the installation in the usegalaxy.eu server for example) if you convert from bedgraph to...
Forum: Bioinformatics 04-16-2018, 06:49 AM
Replies: 1
Views: 1,078
Posted By colindaven
You can probably use the sequences from the CSV...

You can probably use the sequences from the CSV files to create fasta files with a bit of creativity.

Have a look at good text editors like Notepad++ to get this done.

Also check out Galaxy for...
Forum: Bioinformatics 01-18-2018, 04:47 AM
Replies: 1
Views: 1,565
Posted By colindaven
You forgot the main arguments against DRAGEN ...

You forgot the main arguments against DRAGEN

-licenses are limited by throughput
-licenses are REALLY expensive
-licenses are limited by application (buy DNA-seq, can't do RNA-seq).
Forum: Bioinformatics 10-24-2017, 08:28 AM
Replies: 1
Views: 979
Posted By colindaven
This is on bioconda, so I would recommend to...

This is on bioconda, so I would recommend to install via that way:

https://bioconda.github.io/recipes/mapsplice/README.html
Forum: RNA Sequencing 08-11-2017, 12:27 AM
Replies: 4
Views: 2,296
Posted By colindaven
Pooling is always problematic, whether simulation...

Pooling is always problematic, whether simulation is done before or after or not.

I always try to dissuade experimentalists from pooling. There are so many biases in the data anyway. Pools are...
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