SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 16 of 16
Search took 0.01 seconds.
Search: Posts Made By: wbsimey
Forum: General 08-23-2021, 01:24 PM
Replies: 1
Views: 1,299
Posted By wbsimey
Brian Knaus, on his vcfR Git site, helped me...

Brian Knaus, on his vcfR Git site, helped me figure this out. Turns out if you want to include Hardy Weinberg in your population variant calling with bcftools, you must include some annotations with...
Forum: General 08-19-2021, 10:06 AM
Replies: 1
Views: 1,299
Posted By wbsimey
R, vcfr, extrcat.gt, bcftools filter

Hello,
I have been unable to extract depth 'DP' info from my vcf files (generated with latest bcftools variant calling (SNPs)) after being converted to vcfr for R analyses.

bcftools may break the...
Forum: Bioinformatics 01-26-2021, 07:51 AM
Replies: 4
Views: 1,412
Posted By wbsimey
I am using Stacks, they recommend using bwa for...

I am using Stacks, they recommend using bwa for reference based analyses. (https://catchenlab.life.illinois.edu/stacks/manual/#denovobyhand) But, I could not get their recommended pipeline to work,...
Forum: Bioinformatics 01-25-2021, 02:48 PM
Replies: 4
Views: 1,412
Posted By wbsimey
thank you cmbetts! I am running this bash...

thank you cmbetts!

I am running this bash script, which seems to be working and producing many .bam files
for f in $(ls /Projects/RADseq/fastqs/*.gz)
do
bwa mem -t 16...
Forum: Bioinformatics 01-25-2021, 02:06 PM
Replies: 4
Views: 1,412
Posted By wbsimey
mapping hundreds of RADseq fastqs to ref genome.

I would like to map hundreds of fastq.gz single-end RADseq files to a single reference genome.

But, bwa mem is making a map file (.sam) for every fastq file. So I end up with hundreds of...
Forum: Bioinformatics 07-23-2019, 11:16 AM
Replies: 2
Views: 2,914
Posted By wbsimey
bwa GATK4 read group issues

Hello,
I am trying to run GATK4 HaplotypeCaller on bam files from single individuals generated with bwa mem on Ubuntu 18 with
$gatk HaplotypeCaller -R Tse_SBAPGDGG_D.fa -I AHP2746_sorted_dedup.bam...
Forum: Bioinformatics 07-15-2019, 10:29 AM
Replies: 0
Views: 1,865
Posted By wbsimey
mapping multiple low cov genomes to one ref genome

We are starting a project to explore admixture between populations of two species. We have over 40 low coverage genomes (1-5x coverage) (lcg) and a very good reference genome. We have been mapping...
Forum: MGISEQ (FKA Complete Genomics) 08-27-2016, 11:32 AM
Replies: 2
Views: 7,648
Posted By wbsimey
Thank you Luc. When you say "as mentioned in the...

Thank you Luc. When you say "as mentioned in the other post ..." which post are you referring to? Do you have a reference/protocol for whole genome amplification? Can this be done on a multicellular...
Forum: MGISEQ (FKA Complete Genomics) 08-26-2016, 03:21 PM
Replies: 2
Views: 7,648
Posted By wbsimey
WGS prep of micro Eukaryotes

We are planning to sequence a denovo reference genome of a micro Eukaryote, but cannot extract enough DNA from a single individual for PacBio or Nextera Illumina protocols. We have extracted DNA from...
Forum: General 08-26-2016, 03:06 PM
Replies: 1
Views: 2,057
Posted By wbsimey
Micro organism

Hello kmkocot,
we too are planning to sequence a ref genome for a micro eukaryote. Did you ever go forward with your tint invert? and if so, did you use a single individual or did you pool multiple...
Forum: Bioinformatics 12-31-2012, 03:34 PM
Replies: 5
Views: 1,878
Posted By wbsimey
Hi malcook, I tried to run this xargs one-liner,...

Hi malcook, I tried to run this xargs one-liner, but I keep getting a basename error - "basename: invalid option -- 'a'"
I have the latest Ubuntu coreutils (8.13-3ubuntu3.1).
I looked at the...
Forum: Bioinformatics 12-31-2012, 03:08 PM
Replies: 5
Views: 1,878
Posted By wbsimey
Thanks malcook. I will play with this, especially...

Thanks malcook. I will play with this, especially the xargs -P option as I have 32 cores to play with.
Forum: Bioinformatics 12-30-2012, 01:58 PM
Replies: 5
Views: 1,878
Posted By wbsimey
Thank you Justin, that worked perfectly :) As you...

Thank you Justin, that worked perfectly :) As you suggested, I didn't need the 'cp' command.
Forum: Bioinformatics 12-30-2012, 12:02 PM
Replies: 5
Views: 1,878
Posted By wbsimey
Append two fastq files repeatedly

Hello, I am on an Ubuntu 12 system.
I am trying to write a bash loop to run cat /data/rad1/ang_TP30124.fastq /data/rad2/ang_TP30124.fastq > /data/rad3/ang_TP30124.fastq for 184 files.

I have...
Forum: Bioinformatics 09-11-2012, 08:58 AM
Replies: 2
Views: 5,927
Posted By wbsimey
Thank you Dariober, I installed Fastx tools and...

Thank you Dariober, I installed Fastx tools and the trimmer worked perfectly, well, it worked after I figured out the -Q 33 option.
Forum: Bioinformatics 09-10-2012, 06:42 PM
Replies: 2
Views: 5,927
Posted By wbsimey
trim Illumina fastq reads to even read lengths

I have Illumina HiSeq fastq 1.9 files that have been quality trimmed. The sequence lengths range from 90 to 101 bp. I am using the Stacks pipeline, which requires equal length for all reads. Is there...
Showing results 1 to 16 of 16

 


All times are GMT -8. The time now is 03:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO