Moderator: Matt Shirley

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Matt Shirley9.5k
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Cambridge, MA
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http://mattshirley.com/
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mdshw5
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Posts by Matt Shirley

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Answer: A: How to parse a .fasta file in python ?
... 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 Shirley9.5k
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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 11 months ago by Matt Shirley9.5k
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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 12 months ago by Matt Shirley9.5k
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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 19 months ago by Matt Shirley9.5k
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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 23 months ago by Matt Shirley9.5k
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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 23 months ago by Matt Shirley9.5k
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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 2.2 years ago by Matt Shirley9.5k
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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 2.2 years ago by Matt Shirley9.5k
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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 2.4 years ago by Matt Shirley9.5k
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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 2.5 years ago by Matt Shirley9.5k

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
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Good Answer 5 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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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
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Scholar 16 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 19 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 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
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
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 ?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?

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