Moderator: Matt Shirley
Matt Shirley ♦ 8.4k
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Posts by Matt Shirley
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... 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 3 days ago by
Matt Shirley ♦ 8.4k
0
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4
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9.3k
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4
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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 3 months ago by
Matt Shirley ♦ 8.4k
2
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2
answers
603
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2
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... 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
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2
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603
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2
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... What have you tried and what happened? ...
written 4 months ago by
Matt Shirley ♦ 8.4k
0
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5
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509
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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 5 months ago by
Matt Shirley ♦ 8.4k
0
votes
3
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2.1k
views
3
answers
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
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4
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592
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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
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4
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592
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4
answers
... 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
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4
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592
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4
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... 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
676
views
2
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... 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 6 months ago by
Matt Shirley ♦ 8.4k
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For Masking low-complexity regions using pyfaidx MutableFastaRecord
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