Moderator: dariober
dariober ♦ 10k
- Reputation:
- 10,140
- Status:
- Trusted
- Location:
- WCIP | Glasgow | UK
- Website:
- https://github.com/dar...
- Last seen:
- 1 day, 5 hours ago
- Joined:
- 6 years, 8 months ago
- Email:
- d************@gmail.com
about me
Posts by dariober
<prev
• 846 results •
page 1 of 85 •
next >
0
votes
2
answers
79
views
2
answers
... If you are ok with R, have a look at [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html). For something scriptable but with not very polished output see [ASCIIGenome](https://asciigenome.readthedocs.io/en/latest/description.html) (disclaimer- I'm the author) ...
written 9 days ago by
dariober ♦ 10k
0
votes
1
answer
159
views
1
answers
... See edit... Basically, convert ASCII to decimal and from there to quality score using the appropriate offset. Here I use -33 to produce Sanger scores. I don't think it is possible to always decide unambiguously, i.e. automatically, what offset should be used although after reading a few sequencing o ...
written 4 weeks ago by
dariober ♦ 10k
0
votes
1
answer
159
views
1
answers
... Maybe you are making things more complicated than they need in your code. Wouldn't this work?
FastqReader fastqReader = new SangerFastqReader();
File in = new File("fastqfile.fastq");
fastqReader.read(in);
for (Fastq fastq : fastqReader.read(in)) {
String qual = fastq.getQu ...
written 4 weeks ago by
dariober ♦ 10k
4
votes
1
answer
148
views
1
answers
... Hi- I'm not sure if there is a python API for bedops (similar to pybedtools, if this is what you mean). However, in a python script you can use the [subprocess][1] library to execute external commands. E.g. something like (see also [check_call](https://docs.python.org/3/library/subprocess.html#subpr ...
written 8 weeks ago by
dariober ♦ 10k
0
votes
2
answers
258
views
2
answers
... Assuming that by "visualize" you mean showing coverage and/or alignments in genomic windows, you can use [Gviz](http://bioconductor.org/packages/release/bioc/html/Gviz.html) if you are ok with R. For quick, explorative visualization directly from the command line I wrote [ASCIIGenome](https://asciig ...
written 10 weeks ago by
dariober ♦ 10k
0
votes
2
answers
277
views
2
answers
... Keep in mind also that the label "PCR duplicate" is a bit misleading. In fact, it refers to positional duplicates, i.e. reads or read pairs with identical alignment coordinates. As far as I know, in typical Illumina sequencing libraries there is no way to tell apart positional duplicates from PCR du ...
written 3 months ago by
dariober ♦ 10k
0
votes
1
answer
182
views
1
answers
... As far as I know, promoters are still very loosely defined as the regulatory region upstream of a gene, usually 1kb upstream (things are further complicated by the fact that you have multiple transcripts per gene). So to find a promoter in IGV just go to the transcript start site of your gene and pi ...
written 3 months ago by
dariober ♦ 10k
0
votes
1
answer
269
views
1
answers
... Sometimes these sort of questions is best answered by preparing some test cases and see what happens. For example, write a dummy genome of 1000bp with some repeats, write a pair of fastq files with a handful of reads mapping to or near the repeats, index, align and see the results. (In theory, a con ...
written 3 months ago by
dariober ♦ 10k
0
votes
1
answer
706
views
1
answers
Comment:
C: MACS2 option for ATAC seq?
... Hi- My 2p, I just started using [Genrich][1] on ATAC-seq with replicates and my first impression is actually very good when comparing it to MACS2 (I may post a better explanation at some point...).
[1]: https://github.com/jsh58/Genrich ...
written 3 months ago by
dariober ♦ 10k
0
votes
2
answers
202
views
2
answers
... I don't know exactly what's happening with your command but I think to create the arrays you can use something like
array=(`ls -1 /Users/personal/Desktop/blackberry_hybseq_data/Data_and_Nov2018_NZ_assembly/blackberry_hybseq/*gz`)
Then iterate with:
for ((i=0; i<${#array[@]}; ++i));
...
written 4 months ago by
dariober ♦ 10k
Latest awards to dariober
Appreciated
8 days ago,
created a post with more than 5 votes.
For A: Output the color code according to number
Teacher
21 days ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Teacher
25 days ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Teacher
26 days ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Teacher
28 days ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Replace fields CHROM and POS in a vcf file
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Computational Biologist - Cambridge University/CRUK
Cylon
3 months ago,
received 1,000 up votes.
Student
4 months ago,
asked a question with at least 3 up-votes.
For Are ENA and SRA archives in sync?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Computational Biologist - Cambridge University/CRUK
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: Output the color code according to number
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Computational Biologist - Cambridge University/CRUK
Scholar
7 months ago,
created an answer that has been accepted.
For A: Replace fields CHROM and POS in a vcf file
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Computational Biologist - Cambridge University/CRUK
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Librarian
8 months ago,
created a post with more than 10 bookmarks.
For ASCIIGenome: Text Only Genome Viewer!
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Scholar
8 months ago,
created an answer that has been accepted.
For A: Replace fields CHROM and POS in a vcf file
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Appreciated
9 months ago,
created a post with more than 5 votes.
For A: Output the color code according to number
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 999 users visited in the last hour