Admin: Istvan Albert
Istvan Albert ♦♦ 73k
- Reputation:
- 72,540
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 hours ago
- Joined:
- 7 years, 9 months ago
- Email:
- i************@gmail.com
I have published research works in the fields of granular matter physics, network science, machine learning, user interfaces and bioinformatics. But above all I like to create useful systems. I enjoy the process of designing and implementing web based services that stand the test of time. My current project that I dedicate most my time to is an e-book on genomic data analysis:
- The Biostar Handbook - it is modeled by the content on this site and is a comprehensive guide for beginning bioinformaticians.
I am the maintainer of this site:
- Biostar Q&A platform more of a jack-of-all-trades: lead developer, interface designer, database manager, sys admin, dev-ops etc. whatever needs to be done.
Currently I work as a Professor of Bioinformatics at Penn State. Within that position I serve in various roles:
- Director of the Bioinformatics Consulting Center at Penn State
- Bioinformatics instructor
- Researcher and tool developer GeneTrack, and a few others
Posts by Istvan Albert
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... The answer would depend on the scope of the problem and your familiarity with command line tools.
If you only had a few variants at low coverages say 50x, you could visualize the alignments in IGV hover with your mouse on each alignment that indicates a variant and read off the MAPQ. You'd be done ...
written 2 hours ago by
Istvan Albert ♦♦ 73k
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... Variants don't have mapping qualities - the MAPQ refers to alignments.
What you could do however is examine the MAPQ of the alignments that do overlap with your variants and tabulate the MAPQ for these alignments. See if there is a pattern to them.
On the other hand, I would say this is a job that ...
written 3 hours ago by
Istvan Albert ♦♦ 73k
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... first ensure that you assembled the data correctly. I assume you have used stranded RNA-Seq but the nomenclature is confusing (and in the TrueSeq protocols the actual sequence data ends up being generated from the reverse complement) hence it is easy to get the results backward if your parameters ...
written 3 hours ago by
Istvan Albert ♦♦ 73k
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... The next step is to use the argparse library that will allow you to write nice programs that take named parameters like so:
demo.py --organism human --genome hg38 --LTR_cutoff 95 --flanking_cutoff 95
and so on. At that point your program's usage becomes self-documenting.
https://docs.pyth ...
written 4 hours ago by
Istvan Albert ♦♦ 73k
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... the command line parameters will be stored in the module attribute `sys.argv` as a list
import sys
print (sys.argv)
then
python demo.py foo bar this and that
will print
['demo.py', 'foo', 'bar', 'this', 'and', 'that']
...
written 8 hours ago by
Istvan Albert ♦♦ 73k
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... Ther problem with using `raw_input` is that it does not preserve the input that you put in. So it may not cause the problem but it hides the data from you.
Nobody else knows what you have typed in there - you may think you know but it is easy to mistype it.
It is much simpler to list it at the co ...
written 9 hours ago by
Istvan Albert ♦♦ 73k
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... Stop using `raw_input` in programs altoghether. It leads to tedious programs that stop and wait for input. Make your program take parameters from the command line.
my_program.py param1 param2 param3
As for the current program the problem here is that you are adding a comma into the comman ...
written 11 hours ago by
Istvan Albert ♦♦ 73k
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... The purpose of the chromosome file is not to subselect intervals but to indicate how far out to report coverages even if you don't have alignments covering those regions. Hence it is reporting all coverages.
Slice your BAM file to the region of interest (`samtools view -b alignment.bam chr19 > s ...
written 11 hours ago by
Istvan Albert ♦♦ 73k
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... When it comes to IGV some of the colors are not explained well. In addition, these colors may occasionally change slightly.
You kind of get their interpretation of them by trial - most likely means that the distance between paired reads is much larger/smaller than the expected distances computed f ...
written 1 day ago by
Istvan Albert ♦♦ 73k
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Answer:
A: Entrez.esearch url bug
... Something is not right with your setup.
Your code works for me, and, in addition, it is quite unlikely that a variable would be missing inside BioPython. That's really what that says there - it is not an API problem, it is a coding problem that claims that a variable is not initialized at all.
Per ...
written 1 day ago by
Istvan Albert ♦♦ 73k
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