User: jerry

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jerry100
Reputation:
100
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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

<prev • 15 results • page 1 of 2 • next >
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Comment: C: easy-to-use, fast genome browser ?
... 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 jerry100
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easy-to-use, fast genome browser ?
... 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 ...
genome bioinformatics browser written 20 days ago by jerry100 • updated 19 days ago by dariober11k
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Comment: C: Trying to understand samtools -f and -F
... 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 jerry100
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Comment: C: Quality Check of Samples and Biological Replicates
... 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 jerry100
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Answer: A: Quality Check of Samples and Biological Replicates
... 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 jerry100
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Comment: C: How to open HUGE excel files with genomic info
... 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 jerry100
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Comment: C: Best ubuntu version for bioinformatics?
... 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 jerry100
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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 jerry100
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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 jerry100
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Answer: A: Skills & qualities required to be a Bioinformatician
... 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 jerry100

Latest awards to jerry

Supporter 18 days ago, voted at least 25 times.
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Skills & qualities required to be a Bioinformatician

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