User: d-cameron

gravatar for d-cameron
d-cameron1.5k
Reputation:
1,480
Status:
Trusted
Location:
Australia
Last seen:
7 hours ago
Joined:
2 years, 5 months ago
Email:
d***************@gmail.com

Posts by d-cameron

<prev • 176 results • page 1 of 18 • next >
0
votes
1
answer
103
views
1
answers
Comment: C: How can I split the soft clipped reads and map the splitted reads again.
... 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-cameron1.5k
0
votes
0
answers
132
views
0
answers
Comment: C: VCF-simplify: a VCF simplification tool.
... 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-cameron1.5k
0
votes
1
answer
81
views
1
answers
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-cameron1.5k
0
votes
2
answers
101
views
2
answers
Comment: C: Is indel realigning necessary for INDEL discovery?
... 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-cameron1.5k
1
vote
2
answers
184
views
2
answers
Comment: C: Counting soft clipped bases and reads
... 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-cameron1.5k
2
votes
2
answers
184
views
2
answers
Answer: A: Counting soft clipped bases and reads
... 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 ...
written 9 days ago by d-cameron1.5k • updated 9 days ago by h.mon13k
1
vote
1
answer
103
views
1
answers
Comment: C: How can I split the soft clipped reads and map the splitted reads again.
... 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-cameron1.5k
3
votes
2
answers
94
views
2
answers
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-cameron1.5k
2
votes
1
answer
103
views
1
answers
Answer: A: How can I split the soft clipped reads and map the splitted reads again.
... 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-cameron1.5k
0
votes
1
answer
56
views
1
answers
Answer: A: Detecting Overlaps within Grange Object
... >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-cameron1.5k

Latest awards to d-cameron

Scholar 6 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 10 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 19 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 5 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Guru 4 months ago, received more than 100 upvotes.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Centurion 5 months ago, created 100 posts.
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 7 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 10 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 11 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1040 users visited in the last hour