User: d-cameron
d-cameron • 1.9k
- Reputation:
- 1,850
- Status:
- Trusted
- Location:
- Australia
- Last seen:
- 1 month, 1 week ago
- Joined:
- 2 years, 10 months ago
- Email:
- d***************@gmail.com
Posts by d-cameron
<prev
• 216 results •
page 1 of 22 •
next >
0
votes
1
answer
142
views
1
answers
... > gns <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
genes(hg19) returns some really strange results. You'll want to use transcripts() instead as some genes are annotated have two transcripts 100+Mb apart so genes() matches almost the whole chromosome for those.
The clinical pipelines I'm invol ...
written 6 weeks ago by
d-cameron • 1.9k
2
votes
4
answers
288
views
4
answers
... This question is actually very well timed. The GAG4H file formats working group has an upcoming teleconference on the future of VCF and a potential new file format. I strongly recommend getting involved if there are limitations in the existing file formats that make it unsuitable for your use case. ...
written 8 weeks ago by
d-cameron • 1.9k
1
vote
0
answers
141
views
0
answers
... You have redirected the bwa standard error output stream (stderr) to the same location as the standard output stream (stdout. Check your bwa command as redirects such as `2>&1` will do this.
Check your shell configuration as well as some configurations will perform this redirect automaticall ...
written 9 weeks ago by
d-cameron • 1.9k
0
votes
3
answers
269
views
3
answers
... No matter what compressed storage format you use, the majority of the entropy in sequence data is actually in base quality scores, not the actual sequences. If you want 50%+ improvement over fq.gz then you'll be forced to discard information - base quality score binning will make a bigger difference ...
written 9 weeks ago by
d-cameron • 1.9k
0
votes
3
answers
269
views
3
answers
... >it can clip bases, you'll want to relax the defaults
The bases are soft clipped so the information is still there. Only supplementary alignments are hard clipped but the information is in the primary alignment anyway.
>reads could also be filtered if they don't map to the reference genome
...
written 9 weeks ago by
d-cameron • 1.9k
2
votes
1
answer
142
views
1
answers
Comment:
C: How to run IGV
... Run igv.bat from a command prompt to see the error message. ...
written 9 weeks ago by
d-cameron • 1.9k
0
votes
1
answer
147
views
1
answers
... I just use -X 1000 so it works on practically all input libraries. Aren't you getting fewer concordantly alignment reads now? Check the documentation on your simulator (and run picard CollectionInsertSizeMetrics) to see what fragment lengths you've actually simulated.
The community can't agree on w ...
written 9 weeks ago by
d-cameron • 1.9k
0
votes
1
answer
147
views
1
answers
... Unless you've given a custom -X parameter to bowtie2, fragments longer than 500bp are going to be considered discordant. ...
written 9 weeks ago by
d-cameron • 1.9k
2
votes
1
answer
147
views
1
answers
... > See one of my alignment information as below, although it has 100% overall alignment, what is wrong with '1670714 (97.50%) aligned concordantly 0 times'?
Nothing is wrong per se, it's just a combination of bowtie2 incorrectly placed at least one of the reads and/or the fragment size being unus ...
written 9 weeks ago by
d-cameron • 1.9k
1
vote
1
answer
142
views
1
answers
... > what is the optimal strategy to connect these pairs of letters into a sequence
Typically assembler are looking for a [Eulerian path][1], Hamiltonian cycle, or a variation of one of those approaches.
[1]: https://en.wikipedia.org/wiki/Eulerian_path ...
written 9 weeks ago by
d-cameron • 1.9k
Latest awards to d-cameron
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
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.
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.
Scholar
3 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
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.
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
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.
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
5 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Guru
8 months ago,
received more than 100 upvotes.
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Centurion
9 months ago,
created 100 posts.
Good Answer
9 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
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
15 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 911 users visited in the last hour