Moderator: Matt Shirley
Matt Shirley ♦ 8.4k
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Posts by Matt Shirley
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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 12 weeks ago by
Matt Shirley ♦ 8.4k
2
votes
2
answers
564
views
2
answers
... 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 3 months ago by
Matt Shirley ♦ 8.4k
1
vote
2
answers
564
views
2
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... What have you tried and what happened? ...
written 3 months ago by
Matt Shirley ♦ 8.4k
0
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5
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469
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5
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... 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 4 months ago by
Matt Shirley ♦ 8.4k
0
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3
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2.0k
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3
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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 5 months ago by
Matt Shirley ♦ 8.4k
1
vote
4
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574
views
4
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... You're correct. The TPM feature length scaling is taking a few reads and assigning most of the TPM space to them. ...
written 5 months ago by
Matt Shirley ♦ 8.4k
1
vote
4
answers
574
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4
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... I should have been more clear. The issue I solve by using TMM scaling is that because TPM is a unity measure (the sum of all values must be 1e6), highly expressed transcripts/genes in a single sample will **cause all other genes to appear down regulated**, when in fact they are not. TMM normalizatio ...
written 5 months ago by
Matt Shirley ♦ 8.4k
4
votes
4
answers
574
views
4
answers
... Your observation of very short transcripts receiving a disproportionate amount of the TPM is consistent with my observations. It's clear why this is the case. TPM is roughly:
(feature counts / feature length)
/ (sum of [all feature counts / feature lengths]) * 1e6
and so for features with ...
written 5 months ago by
Matt Shirley ♦ 8.4k
4
votes
2
answers
609
views
2
answers
... There are many ways do get sequences from a FASTA file. Some (like the Kent utility) are more efficient than others (reading all sequences into memory and writing them back out). I made a Python library that's designed to be efficient (creates and operates on the same index .fai files that `samtools ...
written 5 months ago by
Matt Shirley ♦ 8.4k
0
votes
3
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1.8k
views
3
answers
... Depending on your use case you might try [simplesam](https://github.com/mdshw5/simplesam). It's a much simpler API than pysam. Your code would become:
fh = simplesam.Reader(open(self.alnfile, 'rb'))
for aln in fh:
print(aln.rname)
You could also filter out unmapped reads by checkin ...
written 5 months ago by
Matt Shirley ♦ 8.4k
Latest awards to Matt Shirley
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22 days ago,
created a question with more than 5,000 views.
For Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
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created a post with more than 5 votes.
For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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3 months ago,
created a question with more than 1,000 views.
For Masking low-complexity regions using pyfaidx MutableFastaRecord
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For Masking low-complexity regions using pyfaidx MutableFastaRecord
Scholar
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created an answer that has been accepted.
For A: How to use pygr? worldbase doesn't return anything
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For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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created an answer that was upvoted at least 5 times.
For A: How Can I Do Principal Components Analysis ?
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For C: What Does 2X250Bp Buy Us?
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For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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For A: Ways To Detect Bias In Dna Sampling For Genomic Sequencing
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For A: How to use pygr? worldbase doesn't return anything
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