User: abascalfederico
abascalfederico • 970
- Reputation:
- 970
- Status:
- Trusted
- Location:
- Spain
- Last seen:
- 5 hours ago
- Joined:
- 2 years, 4 months ago
- Email:
- a**************@gmail.com
Posts by abascalfederico
<prev
• 173 results •
page 1 of 18 •
next >
0
votes
0
answers
100
views
0
answers
... Can anyone recommend a tool to segment the genome according to SNP density (using HMM-based segmentation, for example)?
Thanks!
...
written 16 days ago by
abascalfederico • 970
• updated
9 days ago by
Biostar ♦♦ 20
0
votes
1
answer
202
views
1
answers
... That's exactly what I needed, thanks! ...
written 3 months ago by
abascalfederico • 970
3
votes
1
answer
202
views
1
answer
... Does anybody know of a program to add the NM tag (number of mismatches) to a BAM file?
Usually aligned BAM files come with that tag, but I've found one without it and need that information.
Thanks! ...
written 3 months ago by
abascalfederico • 970
• updated
3 months ago by
trausch • 760
0
votes
0
answers
225
views
0
answers
... I'll send them an email, thanks for the suggestion.
Regarding the use of bwa aln, I found it in the supplementary material of:
Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 hu ...
written 3 months ago by
abascalfederico • 970
4
votes
0
answers
225
views
0
answers
... Anyone knows why in ExAC they used bwa `aln` instead of `mem`? I am not sure of the read lengths but somewhere said something about 150 bps x 2. Does it make sense to use bwa aln here? I though for long reads mem was the best choice
The actual parameters used in ExAC were:
bwa aln q 5 -l 32 -k ...
written 3 months ago by
abascalfederico • 970
3
votes
1
answer
336
views
1
answers
... I know they are popular but Venn diagrams with more than 3 sets are very hard to read!! Why not just a matrix (table) with the numbers for all sets intersections, diagonals having the size of the sets? Or if you want to some graph rather than a table, why not a multidimensionality reduction strategy ...
written 4 months ago by
abascalfederico • 970
1
vote
4
answers
249
views
4
answers
... It seems your key is both, the location and the position. I would use a hash like `$hash{"$location:$position"} = 1`. ...
written 5 months ago by
abascalfederico • 970
0
votes
0
answers
356
views
0
answers
... Python is very popular nowadays (I still do Perl though). Knowing some unix tools is also of great help, including commands like cut, sort, uniq, join, tr and some programming in awk + sed. And of course the R environment/languate for statistics, plotting, scripting...
...
written 5 months ago by
abascalfederico • 970
0
votes
2
answers
319
views
2
answers
Comment:
C: PCA using plink files
... I'd try to add "." to the PATH, or just the full path to "lines" ...
written 5 months ago by
abascalfederico • 970
0
votes
2
answers
319
views
2
answers
Comment:
C: PCA using plink files
... The error message is clear :-) It seems you have to install (or add to your path) a program called "lines"
An alternative to shellfish is [smartpca][1]
[1]: https://github.com/chrchang/eigensoft/blob/master/POPGEN/README ...
written 5 months ago by
abascalfederico • 970
Latest awards to abascalfederico
Popular Question
9 days ago,
created a question with more than 1,000 views.
For Duplicated read names in Fastq file
Popular Question
3 months ago,
created a question with more than 1,000 views.
For List of CNV (copy number variation) regions in the human genome
Student
3 months ago,
asked a question with at least 3 up-votes.
For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Commentator
4 months ago,
created a comment with at least 3 up-votes.
For C: Is it good practice to convert lowewst quality genotyes to missing?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For List of CNV (copy number variation) regions in the human genome
Popular Question
7 months ago,
created a question with more than 1,000 views.
For F3 test for admixture
Commentator
8 months ago,
created a comment with at least 3 up-votes.
For C: Is it good practice to convert lowewst quality genotyes to missing?
Scholar
8 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Scholar
12 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Student
12 months ago,
asked a question with at least 3 up-votes.
For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar
12 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Centurion
16 months ago,
created 100 posts.
Commentator
18 months ago,
created a comment with at least 3 up-votes.
For C: Is it good practice to convert lowewst quality genotyes to missing?
Supporter
19 months ago,
voted at least 25 times.
Scholar
19 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Scholar
19 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: distance between two genes
Scholar
20 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Scholar
20 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: distance between two genes
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: distance between two genes
Scholar
21 months ago,
created an answer that has been accepted.
For A: How to properly merge multiple runs into one bam file ?
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: distance between two genes
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: distance between two genes
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 742 users visited in the last hour