User: User 9996

gravatar for User 9996
User 9996790
Reputation:
790
Status:
Trusted
Location:
Last seen:
6 years, 11 months ago
Joined:
8 years, 6 months ago
Email:
u471

Posts by User 9996

<prev • 63 results • page 1 of 7 • next >
0
votes
3
answers
2.9k
views
3
answers
Comment: C: Best Way To Visualize Linkage And Genetic Map Between Pairs Of Genes?
... WHen I try typing multiple gene names (comma separated) at Jax or use multiple genomic coordinates in the markers box at the end of the form, it just fails with an IndexError or says that no hits match my query. I don't see the "+" button in MapViewer... I have a hard time getting both genes in the ...
written 7.0 years ago by User 9996790
0
votes
3
answers
2.9k
views
3
answers
Comment: C: Best Way To Visualize Linkage And Genetic Map Between Pairs Of Genes?
... @Casey: is there no tool that does this? I cannot figure out MapViewer which was the obvious choice in my mind... I can hack a script to take any two genes, look for nearest SNP based on this table, but it seems like there ought to be a better solution. Especially since that script would be basing i ...
written 7.0 years ago by User 9996790
0
votes
3
answers
2.9k
views
3
answers
Comment: C: Best Way To Visualize Linkage And Genetic Map Between Pairs Of Genes?
... I am fine with using the closest SNP/marker to each gene ...
written 7.0 years ago by User 9996790
0
votes
3
answers
2.9k
views
3
answers
Comment: C: Best Way To Visualize Linkage And Genetic Map Between Pairs Of Genes?
... Which maps should I pick? I find their display very hard to understand though I believe the information should be there, somewhere? ...
written 7.0 years ago by User 9996790
0
votes
3
answers
2.9k
views
3
answers
Comment: C: Best Way To Visualize Linkage And Genetic Map Between Pairs Of Genes?
... this seems far too complicated - I just want to look up the known / empirically estimated recombination frequency between two genes in the mouse genomes... this must be known? ...
written 7.0 years ago by User 9996790
4
votes
3
answers
2.9k
views
3
answers
Best Way To Visualize Linkage And Genetic Map Between Pairs Of Genes?
... What is the best tool to visualize linkage data for a set of genes in the mouse genome? E.g. two genes that are on some chromosome, and you want to get a chromosomal and genetic map of these two genes... how far they are apart on the chromosome, and what the relevant recombination frequencies/centim ...
genome linkage genetics mapping written 7.0 years ago by User 9996790 • updated 7.0 years ago by Mary11k
1
vote
2
answers
4.1k
views
2
answers
Comment: C: Filtering Stream Bam Output Idealy From Pysam/Python
... This will not work since Samfile() needs the first argument to be a filename, and "-" is just a special holder for stdin. So I don't think I can pass it p.stdout ...
written 7.1 years ago by User 9996790
0
votes
2
answers
4.1k
views
2
answers
Comment: C: Filtering Stream Bam Output Idealy From Pysam/Python
... Thanks, but what would I put in the command call to p2 however? I want STDIN to be read from Python, using the Samfile("-", ...) call, so I don't want to capture STDIN into a Python stream (since Pysam unfortunately cannot use that...) ...
written 7.1 years ago by User 9996790
7
votes
2
answers
4.1k
views
5 follow
2
answers
Filtering Stream Bam Output Idealy From Pysam/Python
... I'm making a call to a program that outputs a BAM and I want to filter it on a field. I use Popen() to call the program and then I want to only keep reads that have a certain value for one of the optional SAM/BAM fields. How can this be done from within samtools? Ideally, I'd like to do it from Py ...
python bam samtools written 7.1 years ago by User 9996790 • updated 3.7 years ago by Dan D6.7k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Scoring Repetitive Sequences
... Thanks. Do you know what metrics are used to score sequences that are infact repetitive? ...
written 7.1 years ago by User 9996790

Latest awards to User 9996

Supporter 6.9 years ago, voted at least 25 times.
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Truncating Bam Files With Samtools
Student 7.1 years ago, asked a question with at least 3 up-votes. For Getting Unmapped Reads: Comparing Fastq To Bam
Popular Question 7.8 years ago, created a question with more than 1,000 views. For Fetching Read By Its Id From A Bam File With Pysam In Python
Student 8.5 years ago, asked a question with at least 3 up-votes. For How To Get Number Of Reads In Bam File Efficiently In Python?
Good Question 8.5 years ago, asked a question that was upvoted at least 5 times. For How To Get Number Of Reads In Bam File Efficiently In Python?
Popular Question 8.5 years ago, created a question with more than 1,000 views. For How To Get Number Of Reads In Bam File Efficiently In Python?
Appreciated 8.5 years ago, created a post with more than 5 votes. For How To Get Number Of Reads In Bam File Efficiently In Python?
Student 8.5 years ago, asked a question with at least 3 up-votes. For Getting Genomic Sequences And Phastcons Scores Using Python From Ensembl/Ucsc?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 773 users visited in the last hour