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Forum: Bioinformatics 10-29-2020, 04:58 PM
Replies: 0
Views: 339
Posted By Mark
PacBio software vcf and consensus fasta do not agree

I'm using PacBio's "variantCaller" tool (v6) to call variants on some older RSII subread data I aligned with blasr. The reference is 14845 bp.

My variantCaller command is:

variantCaller...
Forum: Bioinformatics 09-29-2020, 09:02 AM
Replies: 1
Views: 1,120
Posted By Mark
Turns out the problem was, not surprisingly, in...

Turns out the problem was, not surprisingly, in IGV. By default IGV will not show one base pair deletions for what it perceives as PacBio sequence. I had unchecked the "hide indels" box in the...
Forum: Bioinformatics 09-28-2020, 06:53 AM
Replies: 1
Views: 1,120
Posted By Mark
alignment view and vcf disagree

I have a pacbio CCS fastq file that I have aligned to a small (5037 bp) reference which is part of a sequenced BAC clone. I have aligned this data with multiple aligners (minimap2 and smalt), called...
Forum: Bioinformatics 03-01-2018, 06:45 PM
Replies: 1
Views: 2,107
Posted By Mark
BBMAP paired-end alignment problem

Hi All

I'm having a problem with aligning Illumina PE reads with BBMap version 35.92.

Execution of

bbmap.sh overwrite=t ref=Z.fasta in=R1_001_val_1.100.fq in2=R2_001_val_2.100.fq minid=0.25...
Forum: Bioinformatics 10-26-2017, 08:05 AM
Replies: 1
Views: 821
Posted By Mark
Nevermind, I spotted it. This command-line,...

Nevermind, I spotted it. This command-line, which was generated programmatically, contains the following erroneous argument.

-S -1509026240-bowtie2.sam

The hypen in "-1509026240-bowtie2.sam"...
Forum: Bioinformatics 10-26-2017, 07:54 AM
Replies: 1
Views: 821
Posted By Mark
Bowtie2 input read error

Hi All

Bowtie2 is not able to recognize my paired end data input. Seems to be a command line related error but I checked the fastqs anyway and both appear to be fine and properly paired. Note...
Forum: Bioinformatics 08-27-2017, 01:41 PM
Replies: 1
Views: 739
Posted By Mark
Mauve produces no graphic output

Hi

When running progressiveMauve in the latest version of Mauve the alignment appears to be performed as displayed in the Mauve console and finishes with

done.
root alignment has 1...
Forum: Bioinformatics 05-25-2016, 06:02 PM
Replies: 0
Views: 1,066
Posted By Mark
bam file and vcf wildly disagree

Hi All

If anyone can explain this I would appreciate it.

I ran blasr on some pacbio ccs data in fasta format. I then attempted to use freebayes to call variants on the resulting bam file.
...
Forum: Genomic Resequencing 03-22-2016, 05:51 AM
Replies: 1
Views: 5,179
Posted By Mark
freebayes haplotype calling (phased variants)

Hi All

I often use freebayes for variant calling and am pleased with the results. Now I want to use it to call haplotypes. The nature of my project is that I wish to phase variants in 400-450bp...
Forum: Bioinformatics 08-19-2014, 07:32 AM
Replies: 13
Views: 2,373
Posted By Mark
Agreed. Just make a blast db out of your...

Agreed. Just make a blast db out of your scaffolds and blastn them with your gene
Forum: Bioinformatics 08-18-2014, 06:52 PM
Replies: 1
Views: 2,101
Posted By Mark
unexpected bowtie2 unpaired alignment behavior

Hello

Seemingly according to the manual, bowtie2 will attempt to align paired-end reads first as pairs but then as unpaired reads if necessary. If this is so, can someone explain the following. ...
Forum: Bioinformatics 11-02-2013, 05:00 PM
Replies: 3
Views: 2,364
Posted By Mark
RAPsearch2 is 50-100X faster than blastx and...

RAPsearch2 is 50-100X faster than blastx and Pauda claims to be even faster than that
Forum: Bioinformatics 07-13-2013, 07:34 AM
Replies: 14
Views: 2,697
Posted By Mark
Given the head line @VW27N:4:11 lists nothing...

Given the head line
@VW27N:4:11
lists nothing that can be construed as a "1" or "2" designation it seems very likely that you have single end data. Just to be sure, check that the second record in...
Forum: Bioinformatics 07-12-2013, 11:40 AM
Replies: 14
Views: 2,697
Posted By Mark
I was responding to the question on scaffolding...

I was responding to the question on scaffolding single end data. For your question, I've not used ion torrent but if it is similar to illumina output, paired end data comes in two files where single...
Forum: Bioinformatics 07-12-2013, 07:04 AM
Replies: 14
Views: 2,697
Posted By Mark
If you have a related genome to serve as a...

If you have a related genome to serve as a reference you might consider using the bambus2 scaffolder.
Forum: Bioinformatics 07-12-2013, 04:28 AM
Replies: 0
Views: 1,400
Posted By Mark
perplexing bowtie2 repeat alignments

I am seeing something perplexing, can you help? I am trying to call variants in plasmids. To do this I am using bowtie2, freebayes and an assortment of other tools. As a QC I’m initially using...
Forum: Bioinformatics 04-27-2013, 04:49 PM
Replies: 9
Views: 1,619
Posted By Mark
Yea, I know but I don't do the blast updates for...

Yea, I know but I don't do the blast updates for our system and so can't take that route to a fix. Thanks for trying to help though.
Forum: Bioinformatics 04-27-2013, 01:33 PM
Replies: 9
Views: 1,619
Posted By Mark
Subject description. Yes I know you could grab...

Subject description. Yes I know you could grab the oridinal ID and the go back to the blastdb and pull out the record and parse it's description from there but that's a bit of a pain so I would...
Forum: Bioinformatics 04-27-2013, 11:00 AM
Replies: 9
Views: 1,619
Posted By Mark
Unfortunately, you can't get the hit description...

Unfortunately, you can't get the hit description via that method, a serious shortcoming.
Forum: Bioinformatics 04-27-2013, 08:02 AM
Replies: 9
Views: 1,619
Posted By Mark
version 1.006901

version 1.006901
Forum: Bioinformatics 04-26-2013, 10:25 AM
Replies: 9
Views: 1,619
Posted By Mark
bioperl blast parsing problem

We recently upgraded our installation of blast from v2.2.19 to blast+ 2.2.26 and I have found that my bioperl blast xml parsers no longer work properly (typically they return some form of truncated...
Forum: Bioinformatics 03-01-2013, 09:23 AM
Replies: 1
Views: 1,397
Posted By Mark
Please be more explicit. What type of analysis?

Please be more explicit. What type of analysis?
Forum: Bioinformatics 11-11-2012, 01:10 PM
Replies: 5
Views: 5,445
Posted By Mark
IDBA-UD assembler

Hi All

Has anyone given the idba-ud assembler a try? My first go at it produced a bacterial genome assembly quite inferior to what I had achieved with Velvetoptimiser, but proper parameterization...
Forum: Introductions 10-10-2012, 04:43 AM
Replies: 2
Views: 3,395
Posted By Mark
mate pair insert size variation and de novo assembly

Hi All

One of my lab bench colleagues is working on a constructing an Illumina mate pair library intended for use in a target capture procedure where a substantial amount of DNA is needed. ...
Forum: Bioinformatics 10-09-2012, 05:10 AM
Replies: 5
Views: 1,741
Posted By Mark
It's not clear from your post whether de novo or...

It's not clear from your post whether de novo or mapping assembly is best for you. If the organism you are worrking with is well characterized in the regions of interest, then tophat and cufflinks...
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