Moderator: Matt Shirley

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Matt Shirley8.7k
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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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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 days ago by Matt Shirley8.7k
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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 7 days ago by Matt Shirley8.7k
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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 8 weeks ago by Matt Shirley8.7k
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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 3 months ago by Matt Shirley8.7k
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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 3 months ago by Matt Shirley8.7k
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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 3 months ago by Matt Shirley8.7k
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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 4 months ago by Matt Shirley8.7k
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Comment: C: Converting Gvcf Files Into Vcf
... I would try Chris's suggestion, which should really be the accepted answer. ...
written 7 months ago by Matt Shirley8.7k
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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 7 months ago by Matt Shirley8.7k
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Comment: C: How to use pysam to execute "samtools fastq xxx.sam>xxx.fastq"
... What have you tried and what happened? ...
written 7 months ago by Matt Shirley8.7k

Latest awards to Matt Shirley

Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Good Answer 14 days ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How Can I Do Principal Components Analysis ?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Does 2X250Bp Buy Us?
Good Answer 3 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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Popular Question 7 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
Popular Question 9 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
Scholar 9 months ago, created an answer that has been accepted. For A: How to use pygr? worldbase doesn't return anything
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