User: jerry
jerry • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- United States
- Twitter:
- jerryschen31
- Last seen:
- 1 week, 6 days ago
- Joined:
- 5 years, 4 months ago
- Email:
- j****@factorialdx.com
Head of Bioinformatics and Software at Factorial Diagnostics, Inc.
Posts by jerry
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... A command-line genome browser - wonderful idea and impressive, I will try it out!
Yeah, the "pain" is trying to interface with a GUI on a remote server. For now, everyone on the team is just downloading BAM files and installing IGV on their own laptops. But this may be a quick-to-use solution on our ...
written 18 days ago by
jerry • 100
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7 follow
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... Is there an easy-to-use, fast genome browser yet? I have used IGV, and it is painfully slow when trying to load and browse a 50GB whole-genome BAM file. Also, it's not so easy to set up on a remote server for general use. Same thing for UCSC - slow, not easy to set up for general use.
Any other rec ...
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... Perhaps this will help you, from samtools flagstat:
http://www.htslib.org/doc/samtools-flagstat.html
secondary: 0x100 bit set
supplementary: 0x800 bit set
duplicates: 0x400 bit set
mapped: 0x4 bit not set
paired in sequencing: 0x1 bit set
read1: both 0x1 and 0x40 bits set
read2: both 0x1 and ...
written 10 weeks ago by
jerry • 100
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... gene read counts between any two samples, X and Y. This will give you a visual sense of the differences between any two samples, beyond your initial PCA plot. ...
written 10 weeks ago by
jerry • 100
1
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3
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... For those replicates that are very different from each other, you may find it helpful to plot simple X-Y scatter plots. This will tell you if the variance is happening for all ranges of read counts, or only for low-read count genes, or only high-read count genes, etc...
If the replicate scatter plo ...
written 10 weeks ago by
jerry • 100
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4
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... I like this answer, as a way to import an Excel file into a Python script or notebook for analysis. @Mensur Could you comment on how well Pandas read_excel() works? Does it have strange formatting issues with certain types of cells, or fonts, or characters from Excel? ...
written 10 weeks ago by
jerry • 100
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... I would add that it is a good idea to keep a LOG of every program you installed, and how you installed it. For me, I just keep a running list of install commands and download links in a .log file. ...
written 10 weeks ago by
jerry • 100
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1
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Comment:
C: Counting data with ht seq
... Oh I see, understood - will use appropriately next time. Thanks for helping to moderate this forum! ...
written 11 weeks ago by
jerry • 100
0
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Comment:
A: Counting data with ht seq
... I would highly recommend you learn to separate your code into functions. For example:
def htseq_remove_low_genes( file_in, file_out, threshold ):
# output a new file with low genes filtered out
with open(file_in,'r') as f, open(file_out,'w') as fout:
for r in f:
if ...
written 11 weeks ago by
jerry • 100
3
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... Good bioinformaticians have a deep understanding of biology and genomics and are able to use this to either interpret data and uncover insights (for more data-science-driven bioinformaticians) or to develop good tools (for more software-oriented bioinformaticians).
The level of programming skills ...
written 11 weeks ago by
jerry • 100
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