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Search: Posts Made By: lankage
Forum: Bioinformatics 08-26-2016, 08:58 AM
Replies: 651
Views: 134,513
Posted By lankage
Hi, Brian We recently increased our PacBio...

Hi, Brian

We recently increased our PacBio amplicon size from ~1100 to 3kb. With the smaller amplicon size we were able to map reads to our allele reference sequence library of non-full length...
Forum: Bioinformatics 10-28-2015, 08:57 AM
Replies: 651
Views: 134,513
Posted By lankage
mapPacBio.sh - weighting soft clipped mappings higher than mappings with substitution

Hi Brian,
I was wondering if there was a way to adjust the mapping score weights such as to favor a mapping that perfectly maps to a reference with soft clipped ends over a mapping with a number of...
Forum: Bioinformatics 06-30-2015, 09:38 AM
Replies: 651
Views: 134,513
Posted By lankage
>NC_001802DRannotations_(modified)...

>NC_001802DRannotations_(modified)...
Forum: Bioinformatics 06-30-2015, 08:42 AM
Replies: 651
Views: 134,513
Posted By lankage
Hi Brian, Came across an instance today where I...

Hi Brian,
Came across an instance today where I was attempting to parse bbmap SAM output for cigar string information to observe the mapping of some HIV read sequences against a reference. I was...
Forum: Bioinformatics 06-08-2015, 12:02 PM
Replies: 651
Views: 134,513
Posted By lankage
Hi Brian, got another one for you. This time im...

Hi Brian, got another one for you. This time im working with Illumina miseq reads and mapping them to a HIV reference sequence for the purpose of determining the presence or absence of a variety of...
Forum: Bioinformatics 05-28-2015, 10:36 AM
Replies: 651
Views: 134,513
Posted By lankage
mapPacBio.sh - soft clipped mappings

Hi Brian, yet again another question about mapPacBio.sh. I would like to use mapPacBio.sh to map full length MHC allele sequences from pac bio sequencing against a reference dataset which contains...
Forum: Bioinformatics 05-26-2015, 08:11 AM
Replies: 651
Views: 134,513
Posted By lankage
BBmapskimmer.sh

Hi Brian,
I have been experimenting with bbmapskimmer.sh and had a question about flags in the SAM output. I have been looking at a pair of primers matched against the Macaca fasicularis reference...
Forum: Bioinformatics 05-22-2015, 10:29 AM
Replies: 651
Views: 134,513
Posted By lankage
Hi Brian, Thanks for helping with the PacBio...

Hi Brian,
Thanks for helping with the PacBio mapping issues. I have another, unrelated question about usage of bbmap. Is there a way to have bbmap output ALL mappings that meet a certain...
Forum: Bioinformatics 05-15-2015, 12:47 PM
Replies: 651
Views: 134,513
Posted By lankage
Hi Brian, i took your advice with using the...

Hi Brian,
i took your advice with using the "local" parameter with mapPacBio.sh, but I am still seeing reads which perfectly map to a reference in the overlap and have ends that should be soft...
Forum: Bioinformatics 05-12-2015, 08:27 AM
Replies: 651
Views: 134,513
Posted By lankage
bbmap settings

Hi Brian,
I was trying to use bbmap to remap some PacBio reads to some reference sequences in order to generate the detailed cigar string bbmap includes in SAM output. I am trying to generate...
Forum: Bioinformatics 04-10-2015, 11:15 AM
Replies: 2
Views: 740
Posted By lankage
Nevermind - SOLVED

soap3-dp uses the device id as assigned by the CUDA driver installed.
in my /usr/local/cuda/samples ran ./deviceQuery
CUDA shows:
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 7.0,...
Forum: Bioinformatics 04-10-2015, 11:01 AM
Replies: 2
Views: 740
Posted By lankage
soap3-dp using the -c device id option with multiple gpus

Has anyone managed to get soap3-dp's -c option to function correctly? If so what is the format?

-c [GPU device ID] Specify the GPU device for running SOAP3-dp;

2 GeForce GTX 780 Off ...
Forum: Bioinformatics 01-28-2015, 12:42 PM
Replies: 651
Views: 134,513
Posted By lankage
BBTools programs stop reading in fastq reads when encountering 0 length sequences

Brian, found the issue. Our PacBio data contained 0 length sequences that were causing dedupe/bbmap to quit reading in sequences. I removed these and everything runs fine.
Example:
...
Forum: Bioinformatics 01-23-2015, 09:28 AM
Replies: 651
Views: 134,513
Posted By lankage
dedupe.sh question

I recently have been experimenting with read clustering tools using pacbio data. When running dedupe.sh without any of the clustering parameters, I noticed it outputs significantly fewer reads than...
Forum: Pacific Biosciences 11-05-2014, 09:12 AM
Replies: 7
Views: 3,878
Posted By lankage
Great thanks!

Great thanks!
Forum: Pacific Biosciences 11-05-2014, 08:36 AM
Replies: 7
Views: 3,878
Posted By lankage
pac bio quality scores

So a pac bio quality string score of 80 --> "q", is for all intents and purposes equivalent to a score of 41 as far as read quality filtering is concerned?

The tool i want to use attempts to...
Forum: Pacific Biosciences 11-05-2014, 08:24 AM
Replies: 7
Views: 3,878
Posted By lankage
Pac Bio fastq file quality score encoding

I am currently working with fastq files that originated from a pac bio instrument and were converted from their native output format to fastq by some process. This was done at a different site and i...
Forum: Bioinformatics 10-28-2014, 09:45 AM
Replies: 307
Views: 83,871
Posted By lankage
bbduk forcetrimright option

Hi Brian,
Thanks for making the additions! That was exactly what i needed to improve my workflow. One observation i made while looking at differences between the output of bbduk and flexbar is...
Forum: Bioinformatics 10-27-2014, 12:11 PM
Replies: 307
Views: 83,871
Posted By lankage
Version 33.73 BBduk

Thanks alot for the addition! I downloaded version 33.73 of BBtools and I can see the options for restrictleft and restrictright in the help text when running the script with no parameters. I get a...
Forum: Bioinformatics 10-27-2014, 09:41 AM
Replies: 307
Views: 83,871
Posted By lankage
bbduk end trimming

Hi Brian,
I have been trying to use bbduk to trim primer sequences from paired end fastq files and came across a problem. I have been wanting to replace a primer trimming tool, flexbar, with bbduk...
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