User: d-cameron
d-cameron • 740
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Posts by d-cameron
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... Although similar, FASTA and FASTQ are different file formats. FASTQ contains base quality information in addition the sequence information. If you're splitting a FASTQ into many FASTA, you will be discarding sequence quality information. Is this really what you want to do? ...
written 6 weeks ago by
d-cameron • 740
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... It's a historical term from SNP arrays in which the "B" allele probe was the non-reference allele. You are correct in that the B is redundant as pretty much the first thing CNV callers do to allele frequency is convert to minor allelic fraction regardless of whether it was the reference allele or no ...
written 6 weeks ago by
d-cameron • 740
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... >The mutations are supported by the same reads. It's a bit suspicious to me because this could indicate that the reads are from another part of the genome.
It could also indicate that there are three adjacent mutations, or another sort of mutation. Without additional context, is it difficult to ...
written 8 weeks ago by
d-cameron • 740
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... >inflated estimates of translocations
I've found that the majority of false positive translocations are due to sequence homology between the called location. Looking at the extent of the sequence homology around the putative translocation can give you a good indication as to whether the variant ...
written 8 weeks ago by
d-cameron • 740
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6 follow
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... I've been attempting to find a CNV caller for WGS data that utilises both BAF and read depth but there seems to be a dearth of them. I've only managed to find PennCNV-Seq (appear to lack a corresponding publication), Weaver (cancer only, wasted a day failing to get it to run due to severe lack of do ...
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... If you're expecting an insertion-style format, outputting as BEDPE doesn't help as you'd either have to report a pair of translocations (that VCF can already do losslessly) or result to a custom file format.
If you're looking to detect novel sequence insertions then you'd need to use dedicated tool ...
written 8 weeks ago by
d-cameron • 740
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... If you want to assume that all events that look like large insertions are indeed large insertions, then you should look for pairs of translocations in which a pair of translocations events occur at the same location on chrA with different orientations (technically, they with have a 1bp difference if ...
written 8 weeks ago by
d-cameron • 740
1
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... Large insertion of sequence already in the reference, or large insertions of novel sequence (e.g. viral integration)?
>Usually they falsely count them as translocations as well: for exapmle, chr2 to chr1 insertion would be reported as two translocations.
I think you need to revise your expectat ...
written 8 weeks ago by
d-cameron • 740
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... You should only consider this if you cannot get access to the bam files.
The only tool I know of that performs what you're requesting is VCF2CNA http://biorxiv.org/content/early/2017/04/26/131235. I have not used it personally so I cannot vouch that is actually works as advertised.
...
written 8 weeks ago by
d-cameron • 740
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... > I was referring to a deletion on the positive strand for simplicity.
Terminology can be problematic for SVs. A deletion is not 'on the positive strand' - both strands are retained or deleted.
> I though CIGAR strings were for the alignment not the entire read (primary+supplementary)
I use ...
written 9 weeks ago by
d-cameron • 740
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5 weeks ago,
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For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
Teacher
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created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
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created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
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created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
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8 weeks ago,
created an answer that was upvoted at least 5 times.
For A: annotation of SV (Structural Variants)
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9 weeks ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
Scholar
3 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
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4 months ago,
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For A: Please, please, define what a 'read' is.
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4 months ago,
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For A: bwa and bowtie2 bamfile format
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For A: Please, please, define what a 'read' is.
Teacher
4 months ago,
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For A: Please, please, define what a 'read' is.
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
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created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
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For A: Please, please, define what a 'read' is.
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8 months ago,
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For A: bwa and bowtie2 bamfile format
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8 months ago,
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For A: Please, please, define what a 'read' is.
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