Moderator: Matt Shirley

gravatar for Matt Shirley
Matt Shirley8.6k
Reputation:
8,560
Status:
Trusted
Location:
Cambridge, MA
Website:
http://mattshirley.com/
Twitter:
mdshw5
Scholar ID:
Google Scholar Page
Last seen:
22 hours ago
Joined:
7 years, 5 months ago
Email:
m*****@gmail.com

Posts by Matt Shirley

<prev • 703 results • page 1 of 71 • next >
0
votes
3
answers
7.6k
views
3
answers
Comment: C: Get chromosome sizes from fasta file
... `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 7 days ago by Matt Shirley8.6k
0
votes
2
answers
326
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 7 weeks ago by Matt Shirley8.6k
6
votes
2
answers
326
views
2
answers
Answer: A: is this a potential mosaicism?
... For the mother's mosaic allele to be passed to the child you she would need to have the mosaicism present in **her** germline cells. What tissue are you sequencing? If it's a buccal sample or skin punch then it's unlikely that the same developmental progenitor cell that gave rise to the sample you s ...
written 7 weeks ago by Matt Shirley8.6k
0
votes
11
answers
44k
views
11
answers
Comment: C: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
... By default the bash [read](http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_08_02.html) command splits input on newline characters. So in this case `p` will be each incoming line, determined by the `\n` (newline) character. You can change the internal file separator to something like spaces or wha ...
written 9 weeks ago by Matt Shirley8.6k
1
vote
5
answers
15k
views
5
answers
Comment: C: How Do I Convert Fa Files To Bed Format?
... You can accomplish this using `faidx -i bed genome.fa > out.bed`. For more details you can check out the documentation: https://github.com/mdshw5/pyfaidx#cli-script-faidx ...
written 10 weeks ago by Matt Shirley8.6k
0
votes
4
answers
9.8k
views
4
answers
Comment: C: Converting Gvcf Files Into Vcf
... I would try Chris's suggestion, which should really be the accepted answer. ...
written 5 months ago by Matt Shirley8.6k
2
votes
2
answers
738
views
2
answers
Answer: A: How to use pysam to execute "samtools fastq xxx.sam>xxx.fastq"
... If you're going to make a script for this it's not much more effort to go all the way and do the conversion yourself: https://gist.github.com/mdshw5/5cb686a027f805eada61b2b521ab3f13 This uses [simplesam](http://simplesam.readthedocs.io/en/latest/), which has a much simpler (get it?) API than pysam ...
written 6 months ago by Matt Shirley8.6k
1
vote
2
answers
738
views
2
answers
Comment: C: How to use pysam to execute "samtools fastq xxx.sam>xxx.fastq"
... What have you tried and what happened? ...
written 6 months ago by Matt Shirley8.6k
0
votes
5
answers
661
views
5
answers
Answer: A: Rename FASTA files according to FASTA file header
... You can use `pyfaidx` for this: pip install pyfaidx faidx -x input.fasta See [here](https://github.com/mdshw5/pyfaidx/blob/master/README.rst#faidx) for detailed usage. ...
written 7 months ago by Matt Shirley8.6k
0
votes
3
answers
2.2k
views
3
answers
Comment: C: Making bed files from fasta
... I want to point out that this feature didn't work as intended until `pyfaidx` v0.5.2, where someone pointed out that the coordinate weren't 0-based half-open as expected. This has now been fixed: https://github.com/mdshw5/pyfaidx/releases/tag/v0.5.2 ...
written 8 months ago by Matt Shirley8.6k

Latest awards to Matt Shirley

Scholar 8 days ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 5 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 6 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Popular Question 6 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
Popular Question 8 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
Scholar 8 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 9 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: What Does 2X250Bp Buy Us?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 11 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Popular Question 13 months ago, created a question with more than 1,000 views. For On the utility of publishing a tool paper

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1385 users visited in the last hour