Moderator: Matt Shirley
Matt Shirley ♦ 9.5k
- Reputation:
- 9,480
- Status:
- Trusted
- Location:
- Cambridge, MA
- Website:
- http://mattshirley.com/
- Twitter:
- mdshw5
- Scholar ID:
- Google Scholar Page
- Last seen:
- 16 hours ago
- Joined:
- 9 years, 9 months ago
- Email:
- m*****@gmail.com
Posts by Matt Shirley
<prev
• 711 results •
page 1 of 72 •
next >
0
votes
4
answers
168
views
4
answers
... I'll link to my [answer](https://www.biostars.org/p/710/#105492) from almost 7 years ago. Use [biopython](https://biopython.org/wiki/SeqIO) (pure python iterative parsing), [pyfaidx](https://github.com/mdshw5/pyfaidx) (pure python file offset-based parsing), or [pyfastx](https://github.com/lmdu/pyfa ...
written 22 days ago by
Matt Shirley ♦ 9.5k
0
votes
3
answers
3.3k
views
3
answers
... It appears that the original question was a bit vague. The code I provided will replace the first entry in the FASTA file. I'll update the Gist with a bit more information and adapt it to work on a multiFASTA file. ...
written 11 months ago by
Matt Shirley ♦ 9.5k
0
votes
1
answer
417
views
1
answers
Comment:
C: ncbi fasta files
... Do you need to use an HTTP proxy to access the internet? If so, you'll need to set your $HTTP_PROXY and $HTTPS_PROXY environment variables appropriately: https://askubuntu.com/a/584150 ...
written 12 months ago by
Matt Shirley ♦ 9.5k
1
vote
1
answer
19k
views
1
answers
... The two measures are quantifying the same thing: the percentage of a genome that is shared by decent with an ancestor. However PIHAT and Kcoeff can be calculated using different window sizes for consecutive informative SNPS, or can be calculated with or without CNV information, which can help discri ...
written 19 months ago by
Matt Shirley ♦ 9.5k
1
vote
7
answers
113k
views
7
answers
... Thanks. I constantly forget that I'm a moderator. ...
written 23 months ago by
Matt Shirley ♦ 9.5k
2
votes
7
answers
113k
views
7
answers
... The example is *now* wrong, but almost 9 years ago when this was written it was perfectly valid. The Bio.Seq.Seq.tostring() method was removed in the latest Biopython release, and was deprecated a bit before: https://github.com/biopython/biopython/blob/654309121f2cc0c01dfff73cd3dec3a435d76fc2/DEPREC ...
written 23 months ago by
Matt Shirley ♦ 9.5k
1
vote
0
answers
842
views
0
answers
Comment:
C: RNA seq - TMM values
... I think the question was why didn't you go ahead and use edgeR/limma for the statistics part? Most people will use the linear modeling in limma/DESeq2 for statistical testing. ...
written 2.2 years ago by
Matt Shirley ♦ 9.5k
2
votes
1
answer
818
views
1
answers
... You're looking for a gapped representation of the alignment. I'm not sure how to accomplish this in R, but I addressed this issue in the python simplesam package, where you can call the [`gapped` method of a `Sam` object](https://simplesam.readthedocs.io/en/latest/#simplesam.Sam.gapped) to get the s ...
written 2.2 years ago by
Matt Shirley ♦ 9.5k
0
votes
4
answers
20k
views
4
answers
... `faidx` was failing because the cli script expects UCSC-style regions encoded as `contig:start-end`, where `start-end` is optional. Since the HLA alt contains contain `:` characters you ran into a parsing issue. If you want to use `pyfaidx` in the same way as biopython you can do:
from pyfaidx ...
written 2.4 years ago by
Matt Shirley ♦ 9.5k
0
votes
2
answers
1.1k
views
2
answers
Comment:
C: is this a potential mosaicism?
... It's a little more interesting to see this in blood tissue, since there's definitely more mosaicism in blood. If you have access to assays that sequence cell-free DNA, it might be interesting to see if there's an enrichment of the allele in the cfDNA, since this may be shed from some other maternal ...
written 2.5 years ago by
Matt Shirley ♦ 9.5k
Latest awards to Matt Shirley
Appreciated
11 days ago,
created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
Commentator
4 months ago,
created a comment with at least 3 up-votes.
For C: What Does 2X250Bp Buy Us?
Good Answer
5 months ago,
created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Scholar
13 months ago,
created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
Good Answer
14 months ago,
created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Scholar
16 months ago,
created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
Appreciated
17 months ago,
created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Scholar
19 months ago,
created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
Scholar
23 months ago,
created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
Appreciated
2.1 years ago,
created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Good Answer
2.2 years ago,
created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
Good Answer
2.2 years ago,
created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
Good Answer
2.5 years ago,
created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
Appreciated
2.5 years ago,
created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Good Answer
2.5 years ago,
created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
Great Question
2.7 years ago,
created a question with more than 5,000 views.
For Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1854 users visited in the last hour