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Forum: Bioinformatics 07-23-2019, 11:16 AM
Replies: 0
Views: 533
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: 523
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: 3,945
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: 3,945
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: 1,330
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: 1,430
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: 1,430
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: 1,430
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: 1,430
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: 4,859
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: 4,859
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...
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