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Search: Posts Made By: dgscofield
Forum: Bioinformatics 07-02-2017, 07:53 AM
Replies: 6
Views: 2,583
Posted By dgscofield
If you haven't already found a solution, I've got...

If you haven't already found a solution, I've got a simple script that can interconvert between any of the formats supported in BioPerl's Bio::AlignIO, which you'd need to have installed. For Phylip...
Forum: Bioinformatics 10-07-2016, 03:05 PM
Replies: 10
Views: 3,447
Posted By dgscofield
If you have BioPerl ≥ 1.6.922 and...

If you have BioPerl ≥ 1.6.922 and Sort::Naturally, then

https://github.com/douglasgscofield/bioinfo/blob/master/scripts/fastaSort

shows how to sort on sequence name, using natural sort as it...
Forum: Pacific Biosciences 03-03-2016, 02:05 PM
Replies: 2
Views: 1,603
Posted By dgscofield
This thread has some further discussion of this...

This thread has some further discussion of this issue, which we've seen in fungal assemblies. If you have Illumina from the strain you have options for correcting the assembly.
...
Forum: Bioinformatics 02-01-2016, 02:45 PM
Replies: 10
Views: 1,763
Posted By dgscofield
If you have BioPerl available, you could use...

If you have BioPerl available, you could use DISPR (Degenerate In-Silico PcR), which handles degenerate primers just as you have and searches directly within your sequence set of interest.

...
Forum: Bioinformatics 12-18-2015, 02:24 AM
Replies: 6
Views: 4,915
Posted By dgscofield
So that shows characteristics of reads left after...

So that shows characteristics of reads left after removing MAPQ<20? To me those look like reasonable ranges likely arising from biological and/or sequencing causes. As you decrease MAPQ I would...
Forum: Bioinformatics 12-15-2015, 12:17 PM
Replies: 6
Views: 4,915
Posted By dgscofield
Seems reasonable if stringency is what you are...

Seems reasonable if stringency is what you are after. You might be able to also make use of samtools view flags that include (-f) or exclude (-F) certain SAM flags. It's convenient to use...
Forum: Bioinformatics 12-15-2015, 04:59 AM
Replies: 6
Views: 4,915
Posted By dgscofield
I consider the BWA parameters to be worth...

I consider the BWA parameters to be worth tweaking if that is what is required to get "reasonable" alignments of most reads, because of sequencing technology, library characteristics, etc. If...
Forum: Bioinformatics 10-14-2015, 11:31 AM
Replies: 4
Views: 3,114
Posted By dgscofield
We've noticed single-base deletions in PacBio...

We've noticed single-base deletions in PacBio assemblies, via alignment of Illumina reads to otherwise very nice Pacbio assemblies. These occur about every 10^3 to 10^4 bases, and we've also found...
Forum: Bioinformatics 09-26-2015, 12:25 AM
Replies: 4
Views: 2,101
Posted By dgscofield
No, I'm sorry I can't send it to you. You can...

No, I'm sorry I can't send it to you. You can see for yourself that the software includes no explicit license file nor license within any of the source files, so neither I nor other users have been...
Forum: Bioinformatics 09-25-2015, 01:40 PM
Replies: 4
Views: 2,101
Posted By dgscofield
I asked the developers the same question back in...

I asked the developers the same question back in February (tetracker@genoscope.cns.fr). The slclust used is not the sourceforge one, it is their own program.

They sent me a copy, so perhaps you...
Forum: Bioinformatics 08-15-2015, 01:53 AM
Replies: 1
Views: 951
Posted By dgscofield
it would be helpful if you posted the code where...

it would be helpful if you posted the code where you are checking the version.

also, it appears that

print Bio::Perl->VERSION;

is a method call, while

print...
Forum: Bioinformatics 08-06-2015, 11:30 PM
Replies: 4
Views: 979
Posted By dgscofield
BioPerl is great, but unless this is just one...

BioPerl is great, but unless this is just one small task in the midst of several things you want to do with these sequences using BioPerl, I would recommend you turn your coordinate file into BED3...
Forum: Bioinformatics 08-05-2015, 10:41 AM
Replies: 4
Views: 1,462
Posted By dgscofield
i believe it can occur anywhere, and i think you...

i believe it can occur anywhere, and i think you may find that the columns may be empty, but their positions are still delimited with tabs. so that instead of

... <tab> 0 <tab> * <tab> * <tab>...
Forum: Bioinformatics 08-05-2015, 09:04 AM
Replies: 4
Views: 1,462
Posted By dgscofield
It's a longstanding "feature" of samtools mpileup...

It's a longstanding "feature" of samtools mpileup when coverage is 0 because of excluded bases rather than no mapped reads. I would imagine by now there are many scripts that check for this case and...
Forum: Bioinformatics 07-12-2014, 11:56 AM
Replies: 12
Views: 2,614
Posted By dgscofield
As far as other assemblers, we used spades and...

As far as other assemblers, we used spades and mira to assemble the MiSeq data as well but they both took a very very long time, days instead of an hour or so, and as far as we can tell so far (read...
Forum: Bioinformatics 07-12-2014, 11:53 AM
Replies: 12
Views: 2,614
Posted By dgscofield
Pacman, that is spam, I've already reported it. ...

Pacman, that is spam, I've already reported it. Some sort of bot, check the rest of 'Benjamin's posts and they're nonsense.
Forum: Bioinformatics 07-12-2014, 10:13 AM
Replies: 12
Views: 2,614
Posted By dgscofield
And in answer to your question about determining...

And in answer to your question about determining which kmer is configured, the only way I know of is to supply an absurdly large value to the ABYSS executable directly (not the abyss-pe wrapper...
Forum: Bioinformatics 07-12-2014, 10:04 AM
Replies: 12
Views: 2,614
Posted By dgscofield
Yes, and ABySS is very easy to set up. In...

Yes, and ABySS is very easy to set up.

In our national cluster, we have three separate modules of the latest ABySS with different maxk values for each. Perhaps your cluster has something like...
Forum: Bioinformatics 07-12-2014, 09:52 AM
Replies: 12
Views: 2,614
Posted By dgscofield
We've had good results with ABySS on paired-end...

We've had good results with ABySS on paired-end MiSeq for fungal genomes about half that size. You can use longer kmers with ABySS, but you need to specify the maximum size you want when you first...
Forum: Bioinformatics 07-11-2014, 04:32 PM
Replies: 13
Views: 3,295
Posted By dgscofield
CAP3 (http://seq.cs.iastate.edu/cap3.html) is...

CAP3 (http://seq.cs.iastate.edu/cap3.html) is also good for this, you can set identity percentage cutoffs and, though it does end-clipping by default I believe this can be turned off with -k 0. It...
Forum: Bioinformatics 06-05-2013, 04:09 PM
Replies: 3
Views: 2,579
Posted By dgscofield
A bed for your example would be ...

A bed for your example would be


chr1 6384819 6384822
chr1 6384824 6384828

because bed is 0-based, right-open.

You could use my intervalBed script from here...
Forum: MGISEQ (FKA Complete Genomics) 05-23-2013, 03:46 AM
Replies: 1
Views: 6,340
Posted By dgscofield
The link you want is...

The link you want is ftp://ftp.sanger.ac.uk/pub/users/zn1/HI
Forum: Bioinformatics 03-23-2013, 04:50 AM
Replies: 1
Views: 1,444
Posted By dgscofield
For fosmids I've had success with Phrap. Vector...

For fosmids I've had success with Phrap. Vector sequences left over in your fosmid reads can cause misassemblies so clean them (could be difficult) or add the vector to vectors.seq in Phrap to deal...
Forum: Bioinformatics 02-11-2013, 07:59 AM
Replies: 4
Views: 2,156
Posted By dgscofield
Especially if you're after allele frequency...

Especially if you're after allele frequency spectra, estimators are generally better for pooled samples. The 2010 Genetics article by Futschik and Schlötterer...
Forum: Bioinformatics 08-07-2012, 09:39 AM
Replies: 4
Views: 1,848
Posted By dgscofield
I wrote a little Perl script to generate an mlRho...

I wrote a little Perl script to generate an mlRho profile file from samtools mpileup. You can find pileup2pro.pl at https://github.com/douglasgscofield/bioinfo/tree/master/scripts. Bernhard also...
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