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Forum: Bioinformatics 09-17-2014, 02:35 PM
Replies: 11
Views: 3,021
Posted By mchaisso
use celera: http://wgs-assembler.sourceforge.net/

use celera: http://wgs-assembler.sourceforge.net/
Forum: Pacific Biosciences 05-19-2014, 06:34 PM
Replies: 6
Views: 3,457
Posted By mchaisso
Mapping with high error rates is not an issue,...

Mapping with high error rates is not an issue, but there could be edge effects if you are mapping to short contigs. Is this using a short read de novo assembly?

Looking at GC content of the...
Forum: Bioinformatics 12-02-2013, 01:07 PM
Replies: 4
Views: 2,226
Posted By mchaisso
I'm always frustrated to see somebody answer a...

I'm always frustrated to see somebody answer a how-to question by suggesting somebody use a different method, but that's what I'm going to do here.

samtools mpileup is not designed to work with...
Forum: Bioinformatics 10-06-2013, 10:26 PM
Replies: 9
Views: 2,992
Posted By mchaisso
Is there a way to quantify how it is not doing a...

Is there a way to quantify how it is not doing a good job?
Forum: Bioinformatics 09-09-2013, 11:25 AM
Replies: 3
Views: 3,552
Posted By mchaisso
Good comment - it is often good to review the...

Good comment - it is often good to review the sanity of the alignments in a viewer. I neglected to mention that the indels appear in both the paired and unpaired alignments in IGV, as well as bwa...
Forum: Bioinformatics 09-09-2013, 10:26 AM
Replies: 3
Views: 3,552
Posted By mchaisso
bwa mem with paired/unpaired reads

I have a quick question for all bwa mem users (or author, if you have time Heng).

I have some reads from a simulated exome study that have been modified to have a 50/50 allele balance with one...
Forum: Pacific Biosciences 07-15-2013, 01:50 PM
Replies: 3
Views: 3,685
Posted By mchaisso
PacBio produces reads that have different quality...

PacBio produces reads that have different quality values for deletion, insertion, and substitution, so the read are in HDF5 rather than FASTQ.

There is a read simluator called alchemy that is...
Forum: Pacific Biosciences 07-01-2013, 03:08 PM
Replies: 1
Views: 2,342
Posted By mchaisso
I have an unsupported version of BLASR that does...

I have an unsupported version of BLASR that does better alignment across large gaps. I have used this to simply count indel variants (really mobile element insertion) using PacBio reads. PM me if...
Forum: Bioinformatics 06-21-2013, 07:37 AM
Replies: 19
Views: 6,596
Posted By mchaisso
Actually, you start to get closer to correct...

Actually, you start to get closer to correct assemblies using greedy overlap (forming unitigs), so in a sense it is less algorithmically intense to assemble. Finding the overlaps is a bit more...
Forum: Bioinformatics 05-29-2013, 09:54 AM
Replies: 8
Views: 13,411
Posted By mchaisso
I think HGAP is optimized for smaller bacterial...

I think HGAP is optimized for smaller bacterial and bac genomes. Since 130X of 3GB would be about 6 months of runtime on the throughput available 6 months ago on an RS few labs have been willing to...
Forum: Bioinformatics 05-25-2013, 11:58 AM
Replies: 8
Views: 8,950
Posted By mchaisso
Unfortunately, under wrote definition of an...

Unfortunately, under wrote definition of an Eulerian tour, finding a full Eulerian tour is meaningless when there are errors in sequences, and repeats longer than k. The de Bruijn based assemblers...
Forum: Pacific Biosciences 05-25-2013, 11:41 AM
Replies: 6
Views: 3,927
Posted By mchaisso
Hi, we address the same problem in our lab. ...

Hi, we address the same problem in our lab.

There are two solutions, one if you are doing things by hand, the other if you are going to incorporate this into a production pipeline and use ...
Forum: Introductions 05-15-2013, 06:57 AM
Replies: 10
Views: 2,283
Posted By mchaisso
Hi Graham, Nice to see new hackers getting...

Hi Graham,
Nice to see new hackers getting into the field... reminds me of a boggle coding competition back in 1998. Since you are finding all overlaps and not just fixed length k-mers, you may...
Forum: Bioinformatics 04-01-2013, 10:48 AM
Replies: 6
Views: 1,741
Posted By mchaisso
What type of non-Illumina reads? There are now a...

What type of non-Illumina reads? There are now a few categories out there. mrFAST should work for Ion Torrent. If you are using pacbio, the blasr parameter -bestn limits the number of hits you will...
Forum: De novo discovery 03-29-2013, 02:19 PM
Replies: 5
Views: 2,119
Posted By mchaisso
If you have an additional few hundred dollars to...

If you have an additional few hundred dollars to commit to the project, why not just run PacBio sequencing? Since the reads are O(length of the plasmid), it becomes MSA rather than assembly...
Forum: Pacific Biosciences 02-14-2013, 10:16 AM
Replies: 21
Views: 5,849
Posted By mchaisso
Also: A hybrid approach for the automated...

Also: A hybrid approach for the automated finishing of bacterial genomes
http://www.nature.com/nbt/journal/v30/n7/full/nbt.2288.html

PBJelly likely does a better job at getting correct sequences...
Forum: Pacific Biosciences 02-04-2013, 09:47 PM
Replies: 7
Views: 4,842
Posted By mchaisso
These have no meaning to people, and should be...

These have no meaning to people, and should be removed. Sorry they are still there.

best,
-mark
Forum: Pacific Biosciences 02-04-2013, 09:45 PM
Replies: 7
Views: 4,842
Posted By mchaisso
Rather, it's the number cells used in dynamic...

Rather, it's the number cells used in dynamic programming, used to track performance of some of the variable-width banding methods. Nobody should be interested in this (and if I had the power of...
Forum: De novo discovery 01-03-2013, 06:31 PM
Replies: 5
Views: 1,832
Posted By mchaisso
If there were problems with your run, and you...

If there were problems with your run, and you have the budget to resequence with pacbio (probably < $1k), it may make more sense to simply send some DNA to Expression Analysis. With the new...
Forum: Pacific Biosciences 11-15-2012, 09:06 AM
Replies: 5
Views: 3,567
Posted By mchaisso
Perhaps use the pbjelly pipeline to fill gaps? ...

Perhaps use the pbjelly pipeline to fill gaps? Also, with an appropriate pipeline (quiver: https://github.com/PacificBiosciences/GenomicConsensus) you may not need error correction to call accurate...
Forum: General 10-10-2012, 03:05 AM
Replies: 8
Views: 1,889
Posted By mchaisso
In a draft of a recent paper I tried to coin the...

In a draft of a recent paper I tried to coin the term Amplified Cyclic (AC) sequencing for flow cycle sequencing methods (Illumina and IonTorrent), and for single molecule (SM) sequencing, to roll...
Forum: Bioinformatics 06-21-2012, 02:48 PM
Replies: 15
Views: 2,883
Posted By mchaisso
You could say I'm pretty familiar with blasr...

You could say I'm pretty familiar with blasr output ;) (I'm the author).

Most of the help may be found by running blasr -h, or blasr -help for detailed help. There are many output formats...
Forum: Bioinformatics 06-20-2012, 12:50 PM
Replies: 15
Views: 2,883
Posted By mchaisso
bwa sw aligns fasta sequences. You will want...

bwa sw aligns fasta sequences.

You will want the bas.h5 files since they have additional information about subread coordinates.
Forum: Bioinformatics 06-20-2012, 11:58 AM
Replies: 15
Views: 2,883
Posted By mchaisso
Hi Nash, You can install blasr on your own...

Hi Nash,
You can install blasr on your own using github (https://github.com/PacificBiosciences/blasr).

If you have the hdf files, there are options (-useccsdenovo) to align the ccs sequences...
Forum: Bioinformatics 05-25-2012, 10:31 AM
Replies: 5
Views: 3,824
Posted By mchaisso
Hi, right now we're using GMAP to produce spliced...

Hi, right now we're using GMAP to produce spliced alignments. It's a bit slow, but it is fairly sensitive for single pass raw pacbio reads (not ccs and not error corrected), and produces SAM output...
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