User: d-cameron
d-cameron • 1.5k
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Posts by d-cameron
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... The simplest command-line looks like the following:
`java -Xmx512M -cp gridss-VERSION-with-dependencies.jar gridss.SoftClipsToSplitReads I=your_input.bam O=your_output.bam REFERENCE_SEQUENCE=your_reference.fa` ...
written 5 days ago by
d-cameron • 1.5k
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... How does the tool handle SVs? In particular, what happens with variants reported as a) symbolic alleles or b) in breakend notation? ...
written 6 days ago by
d-cameron • 1.5k
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Comment:
C: Remove clipped reads
... It's probably a bit late as you already have a BAM but if you really don't want any read clipped, your probably best off forcing your aligner to align entire reads (e.g. bowtie2 end-to-end). ...
written 9 days ago by
d-cameron • 1.5k
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... It's not 'true' de novo assembly as the reads being assembled have already been mapped to a particular region of the genome. I've done a similar thing for SV calling and I did it without incorporating the reference sequence into the de Bruijn Graph. Whether you do or not, your assembly is already bi ...
written 9 days ago by
d-cameron • 1.5k
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... I've designed it so every step can be run as a stand-alone program. Just run `java -cp gridss.jar gridss.analysis.CollectCigarMetrics`. [example_pipeline.sh][1] has an example of using `CollectGridssMetrics` but `CollectCigarMetrics` works the same way.
[1]: https://github.com/PapenfussLab/grids ...
written 9 days ago by
d-cameron • 1.5k
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... The [GRIDSS][1] package contains a picard-like tool gridss.CollectCigarMetrics which will calculate and summarise the the frequency of each CIGAR element length and operation. Your fraction can then be trivially calculated using read count, and number of reads with 0 soft clip CIGAR elements.
[1 ...
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... I interpreted this as a slightly different question as the other question didn't cover the additional steps required to turn the soft clipped reads + alignments into a split read. You need to:
- match the fragments back to their reads
- drop unmapped fragments - these reads stay as soft clipped re ...
written 10 days ago by
d-cameron • 1.5k
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Answer:
A: What's Supplementary Reads?
... Section 1.2 "Terminologies and Concepts" of the [SAM file format specifications][1] explain this:
> Chimeric alignment
>
>An alignment of a read that cannot be represented
> as a linear alignment. A chimeric alignment is represented as a set of
> linear alignments that do not have la ...
written 10 days ago by
d-cameron • 1.5k
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... I have written a tool to do exact this. [gridss.SoftClipsToSplitReads](https://github.com/PapenfussLab/gridss/releases) extracts the clipped bases and repeatedly realigns them to the reference with the aligner of your choice (default of bwa). The latest development version (currently undergoing inte ...
written 10 days ago by
d-cameron • 1.5k
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... >maxOverlap or minGap
These are exceedingly strange overlap requirements. What are you trying to do? Do you really want to do this?
If you really want these, then you should generate all possible pairings between query and subject, then removing the pairings that satisfy the corresponding minOv ...
written 12 days ago by
d-cameron • 1.5k
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For A: bwa and bowtie2 bamfile format
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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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For A: bwa and bowtie2 bamfile format
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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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For A: annotation of SV (Structural Variants)
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created an answer with at least 3 up-votes.
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For A: Please, please, define what a 'read' is.
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