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Forum: Bioinformatics 05-21-2019, 05:55 AM
Replies: 2
Views: 356
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, 04:44 AM
Replies: 2
Views: 336
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, 05:58 AM
Replies: 2
Views: 372
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, 05:53 AM
Replies: 2
Views: 507
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, 05:45 AM
Replies: 1
Views: 318
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, 03:57 AM
Replies: 2
Views: 499
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, 04:03 AM
Replies: 1
Views: 549
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, 06:27 AM
Replies: 6
Views: 930
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, 03:44 AM
Replies: 2
Views: 656
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, 03:17 AM
Replies: 2
Views: 677
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, 03:50 AM
Replies: 1
Views: 2,098
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, 04:01 AM
Replies: 1
Views: 1,169
Posted By colindaven
STAR or Hisat2, and NOT Tophat2

STAR or Hisat2, and NOT Tophat2
Forum: Bioinformatics 04-16-2018, 06:10 AM
Replies: 13
Views: 1,907
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, 06:05 AM
Replies: 2
Views: 1,262
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, 05:49 AM
Replies: 1
Views: 997
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, 03:47 AM
Replies: 1
Views: 1,329
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, 07:28 AM
Replies: 1
Views: 876
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 08-10-2017, 11:27 PM
Replies: 4
Views: 2,055
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...
Forum: Oxford Nanopore 08-10-2017, 11:21 PM
Replies: 7
Views: 4,144
Posted By colindaven
Good idea. If I were you I'd go for as much...

Good idea. If I were you I'd go for as much Nanopore as I could afford, eg 30X, then create an assembly from this alone using Canu. Then I'd correct the assembly using the nanopore data. In my...
Forum: Bioinformatics 08-04-2017, 04:07 AM
Replies: 1
Views: 1,136
Posted By colindaven
Transdecoder ? http://transdecoder.github.io/

Transdecoder ?

http://transdecoder.github.io/
Forum: SOLiD 08-04-2017, 03:47 AM
Replies: 4
Views: 5,435
Posted By colindaven
I recently found another non-commercial aligner...

I recently found another non-commercial aligner for SOLiD data - it is called subread. I have only tried for Illumina data but it's very good there.

Again, I wouldn't use tophat for such short...
Forum: Bioinformatics 07-24-2017, 06:57 AM
Replies: 5
Views: 1,218
Posted By colindaven
I've done this once using freebayes. It will...

I've done this once using freebayes. It will happily call variants in VCF format from a BAM file with a coverage of 1. Took me a while to find this solution.
Forum: Introductions 06-21-2017, 03:48 AM
Replies: 1
Views: 877
Posted By colindaven
From exomes I have seen on that platform about...

From exomes I have seen on that platform about 50000 good variants are to be expected. 1m is way too high for an exome.

Perhaps you need to filter more on quality, I would recommend filtering with...
Forum: Bioinformatics 12-08-2016, 02:44 AM
Replies: 13
Views: 1,879
Posted By colindaven
There is a decent tool called Circoletto which...

There is a decent tool called Circoletto which might help rechecking your analysis, as it does the blast and circos visualisation itself.

http://tools.bat.infspire.org/circoletto/
Forum: Bioinformatics 12-02-2016, 01:28 AM
Replies: 2
Views: 1,601
Posted By colindaven
It seems you have included a GFF3 file in your...

It seems you have included a GFF3 file in your maker options - one of your conf files. I would recommend supplying evidence as FASTA files to annotate your genome with, so make sure all the GFF3...
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