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Forum: Illumina/Solexa 05-31-2018, 04:12 AM
Replies: 2
Views: 369
Posted By colindaven
Yep, have a look at Flash or bbmerge from the...

Yep, have a look at Flash or bbmerge from the bbmap package to merge R1 and R2 reads.
Forum: Oxford Nanopore 05-31-2018, 03:50 AM
Replies: 1
Views: 444
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: 493
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: 1,463
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: 636
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: 798
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: 705
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: 650
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: 1,251
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: 2,243
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: 795
Posted By colindaven
Transdecoder ? http://transdecoder.github.io/

Transdecoder ?

http://transdecoder.github.io/
Forum: SOLiD 08-04-2017, 03:47 AM
Replies: 4
Views: 4,023
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: 800
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: 595
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: 1,536
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: 1,329
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...
Forum: SOLiD 11-30-2016, 03:43 AM
Replies: 4
Views: 4,023
Posted By colindaven
In general, in comparison to Illumina PE reads...

In general, in comparison to Illumina PE reads don't expect high mapping percentages. From memory I think 50-70% was pretty good, as the data were not extensively filtered (on the 5500xl machine at...
Forum: Bioinformatics 11-16-2016, 06:28 AM
Replies: 4
Views: 1,316
Posted By colindaven
As far as the Minion goes, I was playing with the...

As far as the Minion goes, I was playing with the tool ABruijn yesterday. It worked very well for the bacterial example data and was easy to get going.

https://github.com/fenderglass/ABruijn
...
Forum: Bioinformatics 11-08-2016, 03:22 AM
Replies: 5
Views: 1,124
Posted By colindaven
It's unlikely the alignment or indexing is messed...

It's unlikely the alignment or indexing is messed up across so many aligners. I would suggest the adapter trimming is not working perfectly.

Try using fastqc on your fastq files before and after...
Forum: Bioinformatics 10-25-2016, 02:43 AM
Replies: 2
Views: 982
Posted By colindaven
From memory I think readseq.jar might be able to...

From memory I think readseq.jar might be able to help, it is simple too.

http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
Forum: Bioinformatics 09-06-2016, 04:03 AM
Replies: 15
Views: 2,162
Posted By colindaven
Any details, was fraud or misconduct alleged here...

Any details, was fraud or misconduct alleged here ?
Forum: Bioinformatics 08-12-2016, 01:14 AM
Replies: 4
Views: 1,271
Posted By colindaven
I got quite a long way with this script: ...

I got quite a long way with this script:

https://github.com/PacificBiosciences/FALCON/issues/251

Also had to remove duplicates
Forum: Bioinformatics 08-03-2016, 11:12 PM
Replies: 1
Views: 921
Posted By colindaven
I don't know of anything here. de novo assembly...

I don't know of anything here. de novo assembly is very tricky with SOLiD and actually doesn't work at all. You can expect very short transcript fragments (<1kbp, most ~200bp). Illumina works a lot...
Forum: Bioinformatics 07-01-2016, 02:34 AM
Replies: 2
Views: 1,064
Posted By colindaven
Sounds tricky - have you tried tadpole - listed...

Sounds tricky - have you tried tadpole - listed on this forum - yet ?
Forum: Bioinformatics 06-20-2016, 05:56 AM
Replies: 7
Views: 2,975
Posted By colindaven
Thanks, that's a great answer. I will look at...

Thanks, that's a great answer. I will look at looking DEIVA in the future if it is easy to install since there is a lot of value in this kind of app where a biologists' exploration of their own data...
Showing results 1 to 25 of 399

 


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