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Moderator: Matt Shirley

gravatar for Matt Shirley
Matt Shirley ♦ 9.1k
Reputation:
9,050
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Trusted
Location:
Cambridge, MA
Website:
http://mattshirley.com/
Twitter:
mdshw5
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Google Scholar Page
Last seen:
4 days, 18 hours ago
Joined:
8 years, 4 months ago
Email:
m*****@gmail.com

Posts by Matt Shirley

<prev • 708 results • page 1 of 71 • next >
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Comment: C: Ibd (Identity By Descent) And The Chosen Value Of Pi_Hat
... 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 8 weeks ago by Matt Shirley ♦ 9.1k
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Comment: C: Correct Way To Parse A Fasta File In Python
... Thanks. I constantly forget that I'm a moderator. ...
written 5 months ago by Matt Shirley ♦ 9.1k
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Comment: C: Correct Way To Parse A Fasta File In Python
... 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 5 months ago by Matt Shirley ♦ 9.1k
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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 9 months ago by Matt Shirley ♦ 9.1k
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Answer: A: Get sequences from a BAM file as strings spaced out as described by cigar
... 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 9 months ago by Matt Shirley ♦ 9.1k
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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 11 months ago by Matt Shirley ♦ 9.1k
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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 12 months ago by Matt Shirley ♦ 9.1k
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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 12 months ago by Matt Shirley ♦ 9.1k
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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 13 months ago by Matt Shirley ♦ 9.1k
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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 13 months ago by Matt Shirley ♦ 9.1k

Latest awards to Matt Shirley

Scholar 8 weeks ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Scholar 6 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Appreciated 7 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 ?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Scholar 11 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Great Question 14 months ago, created a question with more than 5,000 views. For Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 16 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 16 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Popular Question 17 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
Popular Question 18 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
Scholar 19 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Appreciated 20 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
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