Moderator: Matt Shirley

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Matt Shirley9.3k
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Cambridge, MA
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http://mattshirley.com/
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9 years, 2 months ago
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Posts by Matt Shirley

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Comment: C: change specific bases in a fasta file
... 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 4 months ago by Matt Shirley9.3k
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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 5 months ago by Matt Shirley9.3k
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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 12 months ago by Matt Shirley9.3k
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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 16 months ago by Matt Shirley9.3k
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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 16 months ago by Matt Shirley9.3k
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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 19 months ago by Matt Shirley9.3k
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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 20 months ago by Matt Shirley9.3k
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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 21 months ago by Matt Shirley9.3k
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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 23 months ago by Matt Shirley9.3k
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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 23 months ago by Matt Shirley9.3k

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Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Scholar 6 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Good Answer 8 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 9 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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Scholar 12 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
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Scholar 17 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Appreciated 18 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 ?
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Scholar 21 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
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
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Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing

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