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Search: Posts Made By: Gopo
Forum: Bioinformatics 12-04-2018, 03:53 AM
Replies: 1
Views: 435
Posted By Gopo
I wonder if the repetitive content of the two...

I wonder if the repetitive content of the two genomes had anything to do with the unexpected results with Velvet Columbus?
Forum: Bioinformatics 11-13-2018, 11:23 PM
Replies: 5
Views: 518
Posted By Gopo
Sorry, I don't know of a solution. The best I can...

Sorry, I don't know of a solution. The best I can suggest is to report this to the issues page on the Picard github repo.
https://github.com/broadinstitute/picard/issues

Again, maybe a newer...
Forum: Bioinformatics 11-12-2018, 02:35 AM
Replies: 5
Views: 518
Posted By Gopo
I am not sure I understand what you are trying to...

I am not sure I understand what you are trying to do. Are you trying to merge the mapped paired-end reads BAM file with the mapped single-end reads BAM file? Perhaps a newer version of Picard might...
Forum: Bioinformatics 11-07-2018, 03:47 AM
Replies: 5
Views: 518
Posted By Gopo
bwa index -a bwtsw genome.fasta Usage: bwa...

bwa index -a bwtsw genome.fasta

Usage: bwa index [options] <in.fasta>

Options: -a STR BWT construction algorithm: bwtsw or is [auto]
-p STR prefix of the index [same as fasta...
Forum: Pacific Biosciences 10-27-2018, 04:56 AM
Replies: 5
Views: 874
Posted By Gopo
Here is a script for running Pilon twice quickly...

Here is a script for running Pilon twice quickly by splitting the genome to be corrected into parts, generating intervals for Pilon to hasten its processing, and combining them again

It assumes...
Forum: Pacific Biosciences 10-22-2018, 11:13 PM
Replies: 5
Views: 874
Posted By Gopo
I have a GIST that should help you with...

I have a GIST that should help you with instructions that I used for running PBJelly and then correct indels (not with Pilon but with a variant caller)- see...
Forum: Pacific Biosciences 10-20-2018, 06:53 AM
Replies: 5
Views: 874
Posted By Gopo
For the PacBio Sequel data, were you using the...

For the PacBio Sequel data, were you using the raw subreads? That's what I would recommend. By default the PacBio subread BAM files give a quality score of Q0 to all bases, and PBJelly needs quality...
Forum: Bioinformatics 08-08-2018, 11:11 PM
Replies: 4
Views: 1,188
Posted By Gopo
You will have to make the BED file yourself. Here...

You will have to make the BED file yourself. Here is a guide:


# install picard
cd ~/bin/
wget https://github.com/broadinstitute/picard/releases/download/2.18.10/picard.jar
mv picard.jar...
Forum: Bioinformatics 08-07-2018, 03:58 AM
Replies: 4
Views: 1,188
Posted By Gopo
Try CollectHSmetrics - part of Picard Tools For...

Try CollectHSmetrics - part of Picard Tools
For details see:
https://broadinstitute.github.io/picard/command-line-overview.html
Forum: Bioinformatics 04-26-2018, 10:35 PM
Replies: 658
Views: 140,533
Posted By Gopo
Hi Brian, Does bbmap callvariants.sh ignore...

Hi Brian,

Does bbmap callvariants.sh ignore duplicates marked by picard MarkDuplicates by default (or is there an option to ignore duplicates) or do duplicates have to be deleted?

Best,
Gopo
Forum: Bioinformatics 02-11-2018, 10:56 PM
Replies: 3
Views: 822
Posted By Gopo
So, I had this problem- it could be due to two...

So, I had this problem- it could be due to two things:
(1) By default BUSCO has a file called /path-to-busco-installation/busco/config/config.ini.default. That file needs to modified and renamed as...
Forum: Genomic Resequencing 02-04-2018, 03:06 AM
Replies: 2
Views: 2,803
Posted By Gopo
As far as I know, Agilent will not confirm or...

As far as I know, Agilent will not confirm or deny any of their bait library concentrations.
Forum: General 01-23-2018, 12:11 PM
Replies: 3
Views: 1,090
Posted By Gopo
Unfortunately, I can't really give too much...

Unfortunately, I can't really give too much advice about optimizing. Others on the forum have more experience than I do. I've personally subsampled a dataset of 16 individuals, 4 per population,...
Forum: General 01-23-2018, 11:43 AM
Replies: 3
Views: 1,090
Posted By Gopo
If I understand you correctly, your samples could...

If I understand you correctly, your samples could be up to 100 years old? Depending on the source of DNA, the DNA maybe sheared and low molecular weight, making it less amenable to ddRAD. If this is...
Forum: Bioinformatics 01-23-2018, 01:15 AM
Replies: 25
Views: 16,819
Posted By Gopo
I am not sure this is a bug or not, but when I...

I am not sure this is a bug or not, but when I try to use reformat.sh (version 37.76) to add fake qualities of Q30 to a PacBio Sequel fastq file (produced with bamtools convert -format fastq -in...
Forum: Bioinformatics 11-02-2017, 07:30 AM
Replies: 97
Views: 23,021
Posted By Gopo
Hi Brian, I recreated the paired-end FASTQ...

Hi Brian,

I recreated the paired-end FASTQ files, performed adapter and quality trimming with bbduk, then used tadpole for error correction, and finally used tadpole in contig mode to de novo...
Forum: Bioinformatics 10-13-2017, 01:49 PM
Replies: 97
Views: 23,021
Posted By Gopo
Hi Brian, I used bbmerge and am now trying...

Hi Brian,

I used bbmerge and am now trying to error correct my paired and merged reads with tadpole at the same, but I can't seem to get the right syntax for the input

I tried the following...
Forum: Bioinformatics 10-13-2017, 11:40 AM
Replies: 97
Views: 23,021
Posted By Gopo
Hi Brian, no it did not crash- unfortunately the...

Hi Brian, no it did not crash- unfortunately the job exceeded the allowed walltime. I'll try what you suggested for Tadpole first.

@GenoMax - Thank you. Unfortunately, they were unable to finish...
Forum: Bioinformatics 10-13-2017, 10:49 AM
Replies: 97
Views: 23,021
Posted By Gopo
No I haven't, but based on the manual- I am out...

No I haven't, but based on the manual- I am out of luck as ALLPATHS-LG requires shotgun sequencing and mate pair libraries.
Forum: Bioinformatics 10-13-2017, 01:37 AM
Replies: 97
Views: 23,021
Posted By Gopo
Hi Brian, Does Tadpole have a checkpoint...

Hi Brian,

Does Tadpole have a checkpoint option, or this a possible feature to add? I ask because I am de novo assembling the axolotl genome using the available raw paired end shotgun sequencing...
Forum: Bioinformatics 10-10-2017, 03:33 AM
Replies: 658
Views: 140,533
Posted By Gopo
Hi Brian, GATK does output "./." for...

Hi Brian,
GATK does output "./." for individuals where a genotype can't be reliably called at a particular SNP (can't remember if freebayes and/or ANGSD does this too). What is the flag for "PF"...
Forum: Bioinformatics 10-06-2017, 05:04 AM
Replies: 658
Views: 140,533
Posted By Gopo
Hi Brian, I really like callvariants.sh...

Hi Brian,
I really like callvariants.sh (simulated di-allelic SNPs and at both low (4x) and moderate (60x) sequencing coverage, filtering to keep only variants with quality score of >=Q27,...
Forum: Bioinformatics 06-12-2017, 10:54 AM
Replies: 3
Views: 852
Posted By Gopo
Hi Brian, Like Sven, I am also interested in...

Hi Brian,

Like Sven, I am also interested in using error correction- albeit for a different purpose, which may or may not be appropriate given the context.

So, I am analyzing SuperSage...
Forum: Bioinformatics 03-24-2017, 08:34 AM
Replies: 2
Views: 1,775
Posted By Gopo
PGDSpider doesn't name the loci in its list, so I...

PGDSpider doesn't name the loci in its list, so I used the make_bayescan_input.py script from The Simple Fool's Guide to Population Genomics via RNA-Seq available at...
Forum: Bioinformatics 02-15-2017, 09:13 AM
Replies: 4
Views: 830
Posted By Gopo
sangerseqR can parse AB1 files. It doesn't have...

sangerseqR can parse AB1 files. It doesn't have built in functions to cut 50bp, but you could probably cobble something together with Bioconductor....
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