Moderator: Matt Shirley

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Matt Shirley8.4k
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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 Shirley8.4k
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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 3 months ago by Matt Shirley8.4k
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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 3 months ago by Matt Shirley8.4k
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Answer: A: Rename FASTA files according to FASTA file header
... 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 Shirley8.4k
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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 Shirley8.4k
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Comment: C: A very short gene with very high TPM
... 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 Shirley8.4k
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Comment: C: A very short gene with very high TPM
... 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 Shirley8.4k
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Answer: A: A very short gene with very high TPM
... 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 Shirley8.4k
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Answer: A: How to extract specific genes from a fasta file
... 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 Shirley8.4k
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Answer: A: Pysam is giving - ValueError: reference_id -1 out of range 0<=tid<65334. Any su
... 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 Shirley8.4k

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Popular Question 3 months ago, created a question with more than 1,000 views. For Masking low-complexity regions using pyfaidx MutableFastaRecord
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