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Search: Posts Made By: Gopo
Forum: Bioinformatics 10-02-2019, 03:53 AM
Replies: 3
Views: 808
Posted By Gopo
Personally, I would do quality and adapter...

Personally, I would do quality and adapter trimming (and maybe error-correction) of the raw Illumina reads as MaSuRCA pretty much does this from what I understand and use the quality and adapter...
Forum: Bioinformatics 09-04-2019, 12:18 AM
Replies: 1
Views: 742
Posted By Gopo
I would call SNPs with your desired variant...

I would call SNPs with your desired variant caller (I prefer CallVariants from BBTools/BBMap) then use bedtools intersect (-a study.vcf.gz -b bed-file-of-snps) and the output is a VCF file of...
Forum: Bioinformatics 09-02-2019, 02:42 AM
Replies: 2
Views: 624
Posted By Gopo
No this is not common, but MAKER's...

No this is not common, but MAKER's (http://www.yandell-lab.org/software/maker.html) gff3_merge script can output a GFF file with FASTA sequence at the end.
Forum: Bioinformatics 05-02-2019, 05:23 AM
Replies: 2
Views: 915
Posted By Gopo
Suggestions would depend on many factors such as...

Suggestions would depend on many factors such as how closely-related the reference is your current genome. See https://www.biostars.org/p/341670/#347747 for some suggestions. I have had good results...
Forum: Bioinformatics 04-29-2019, 12:09 AM
Replies: 1
Views: 729
Posted By Gopo
For the second round, you first need to create a...

For the second round, you first need to create a new .bam file using the .fasta output of the first round as template.

Here is a script (hosted on GitHub gist) for running Pilon twice on a single...
Forum: RNA Sequencing 04-15-2019, 05:38 AM
Replies: 3
Views: 1,897
Posted By Gopo
Sounds logical, but not sure. This article might...

Sounds logical, but not sure. This article might be of interest...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2745-1
Forum: Bioinformatics 04-09-2019, 01:26 AM
Replies: 1
Views: 625
Posted By Gopo
You might be able to find some more resources on...

You might be able to find some more resources on your bcftools pipeline on www.biostars.org. Just query for bcftools variant calling or something to see if you can find more resources.
Forum: Illumina/Solexa 03-13-2019, 12:33 AM
Replies: 3
Views: 682
Posted By Gopo
The "fragment" of 1000bp in your example would be...

The "fragment" of 1000bp in your example would be flanked by sequencing adapters in traditional Illumina sequencing, but really, you would call what you are calling the "fragment" as the insert...
Forum: Bioinformatics 12-04-2018, 03:53 AM
Replies: 1
Views: 784
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: 1,209
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: 1,209
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: 1,209
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: 2,923
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: 2,923
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: 2,923
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: 2,409
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: 2,409
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: 678
Views: 184,750
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: 1,334
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: 4,894
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: 1,513
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: 1,513
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: 35
Views: 25,565
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: 104
Views: 34,676
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: 104
Views: 34,676
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...
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