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Forum: Pacific Biosciences Today, 05:53 AM
Replies: 1
Views: 105
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, 10:11 PM
Replies: 4
Views: 908
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, 02:58 AM
Replies: 4
Views: 908
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, 09:35 PM
Replies: 651
Views: 134,517
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, 09:56 PM
Replies: 3
Views: 769
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, 02:06 AM
Replies: 2
Views: 2,502
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, 11:11 AM
Replies: 3
Views: 965
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, 10:43 AM
Replies: 3
Views: 965
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, 12:15 AM
Replies: 25
Views: 15,876
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, 06:30 AM
Replies: 97
Views: 21,721
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, 12:49 PM
Replies: 97
Views: 21,721
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, 10:40 AM
Replies: 97
Views: 21,721
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, 09:49 AM
Replies: 97
Views: 21,721
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, 12:37 AM
Replies: 97
Views: 21,721
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, 02:33 AM
Replies: 651
Views: 134,517
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, 04:04 AM
Replies: 651
Views: 134,517
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, 09:54 AM
Replies: 3
Views: 782
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, 07:34 AM
Replies: 2
Views: 1,611
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, 08:13 AM
Replies: 4
Views: 782
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....
Forum: Sample Prep / Library Generation 08-12-2014, 06:55 PM
Replies: 9
Views: 4,723
Posted By Gopo
superduper - did you use XT blockers with the XT...

superduper - did you use XT blockers with the XT hyb mix and get okay results? I ask because XT2 adapters contain 8bp indexes while XT adapters have 6bp indices, so both kits would presumably use...
Forum: Sample Prep / Library Generation 08-07-2014, 04:51 PM
Replies: 9
Views: 4,723
Posted By Gopo
superduper - thanks for the info! The same group...

superduper - thanks for the info! The same group has a homebrew recipe for an AMpure XP substitute http://protocols-serapure.readthedocs.org/en/latest/
...
Forum: Sample Prep / Library Generation 04-15-2014, 05:00 AM
Replies: 9
Views: 4,723
Posted By Gopo
bwubb - Curious if you could share your results....

bwubb - Curious if you could share your results. Did you have to add 3x more XT bait library volume in the hybridization reactions with XT2 reagents (i.e., 15uL baits instead of 5uL) or have to...
Forum: RNA Sequencing 01-11-2014, 06:12 AM
Replies: 3
Views: 1,705
Posted By Gopo
I cannot comment on the final step but have...

I cannot comment on the final step but have performed steps 1-3 using the tool GOanna http://www.agbase.msstate.edu/cgi-bin/tools/GOanna.cgi and then used the resulting GO slim file and custom python...
Forum: Bioinformatics 11-20-2013, 06:43 AM
Replies: 1
Views: 904
Posted By Gopo
You might want to give GOanna a try ...

You might want to give GOanna a try

http://www.agbase.msstate.edu/cgi-bin/tools/GOanna.cgi
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