Admin: Istvan Albert
Istvan Albert ♦♦ 82k
- Reputation:
- 81,820
- Status:
- Trusted
- Location:
- University Park, USA
- Website:
- https://www.ialbert.me/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 19 hours ago
- Joined:
- 10 years, 4 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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... I think the right solution is probably to read your files with a programming interface like Pysam and work out the issues that way.
https://pysam.readthedocs.io/en/latest/api.html
...
written 14 days ago by
Istvan Albert ♦♦ 82k
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... Is it possible that you have two reads with the same name (since it is paired) and the other raises the error?
Also see if `bam2bed` followed by a `bed2bam` would work (`bedtools`) ...
written 14 days ago by
Istvan Albert ♦♦ 82k
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... The problem here goes much deeper. Simply put most statistical methods cannot account for the type of errors you observe.
The concept of transcript integrity as described here:
http://rseqc.sourceforge.net/#tin-py
is the closest to what you might be after. What you want is to filter not just for ...
written 14 days ago by
Istvan Albert ♦♦ 82k
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...
The "normal" expectation for NGS data is that no reads have adapters in them. The explanation for not having adapters is that the DNA fragment is longer than the read length.
The "typical" adapter read-through is an "error" that happens when the instrument gets a DNA fragment that is too short.
U ...
written 15 days ago by
Istvan Albert ♦♦ 82k
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... I would say that the data shows too many reads in the intronic regions (your second image) - 10 to 20% of the exonic read counts are present.
Also, there is unexpectedly weird fragmentation throughout - coverages drop the zero in the middle of the exon.
...
written 15 days ago by
Istvan Albert ♦♦ 82k
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Comment:
C: Command prompts combination
... It is not clear what you are saying here, the commands do work separately but not when giving the command together?
In what way does it not work?
Do one step at a time, see if you can get it to work - most importantly the files need to be sorted by the field that you join on. ...
written 16 days ago by
Istvan Albert ♦♦ 82k
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... Don't put `LC_ALL=C` as a parameter to blast! That won't work.
You can set LC_ALL=C before a command:
LC_ALL=FOO; echo $LC_ALL
prints:
FOO
it gets applied to all commands run in that shell.
The best recommendation would be to export the variable in bash (preferable upon initialization ...
written 17 days ago by
Istvan Albert ♦♦ 82k
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... take a screenshot of a gene/transcript that comes up differentially expressed and show it here.
show the coverages for both tracks the control and condition, here is an example (host with imgur):
![enter image description here][1]
[1]: https://i.imgur.com/BRuwP7a.png ...
written 17 days ago by
Istvan Albert ♦♦ 82k
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Comment:
C: Paired end for minia
... This sounds like there may be contaminations and other errors in the data. As you add more data the number of systematic errors increases. It also often happens that the second in pair is worse in quality (though nowadays that is rarer).
Evaluate your data with FastQC, see if you need to clean it u ...
written 18 days ago by
Istvan Albert ♦♦ 82k
0
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Comment:
A: Paired end for minia
... Don't concatenate the reads.
If you believe that the reads overlap use a tool that merges your paired-end reads into one. ...
written 18 days ago by
Istvan Albert ♦♦ 82k
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