User: billzt

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billzt20
Reputation:
20
Status:
New User
Location:
Australia
Last seen:
2 years, 6 months ago
Joined:
4 years, 11 months ago
Email:
b*****@hotmail.com

Posts by billzt

<prev • 12 results • page 1 of 2 • next >
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(Closed) Visualization of transcript structure like Ensembl
... I have GFF data for transcript structure annotations, and I want to visualize the exon-intron-UTR-CDS structures  of  the transcripts on webpages like Ensembl, which seems really cool. Any good tools to recommend? Thanks!     ...
gene genome sequence written 3.4 years ago by billzt20 • updated 3.4 years ago by Prakki Rama2.2k
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Answer: A: Recommended data warehouse tools for bioinformatics search?
... All the data had been stored on local server, in FASTA, GFF, or tab delimited files. They could be dumped into databases. We want to implement data search frontends like the "key word search" and "gene page" of Phytozome or Metazome. ...
written 3.6 years ago by billzt20
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Recommended data warehouse tools for bioinformatics search?
... I'm a bioinformatician with some Perl programming skills. However other members in my lab didn't know much about bioinformatics. Sometimes they need to search for some specific gene IDs and obtain their sequences, structures (GFF) and GO annations. As the organisms are non-model species, public serv ...
genome gene sequence written 3.6 years ago by billzt20 • updated 3.6 years ago by Jean-Karim Heriche18k
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Picard remove duplicate leads to some unpaired reads
... Hi to all. I have a Illuminna pair-end reads mapping result in bam format. I use picard to remove PCR duplicate reads: java -jar picard.jar MarkDuplicates INPUT=a.sortpos.bam OUTPUT=a.rmdup.bam METRICS_FILE=a.rmdup.log REMOVE_DUPLICATES=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 Then I use bamTo ...
duplicate next-gen picard written 3.7 years ago by billzt20
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Answer: A: Counting Number Of Bases In A Fastq File
... Please try this: https://github.com/billzt/readfq Smart and Fast!!! ...
written 3.7 years ago by billzt20
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How to estimate peak memory usage of SOAPdenovo
... Hello to everyone. As I need to rent servers to run SOAPdenovo, I have to know how much physical memory I need, given on my genome size (~2G), my data ( Illumina PE ~200G) and my kmer size (63). I was glad to share other parameters if needed. Thank you! ...
assembly soapdenovo memory written 3.9 years ago by billzt20 • updated 3.9 years ago by Brian Bushnell16k
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(Closed) How to control other factors when using Fisher's exact test
... I use Fisher's exact test a lot. Here is an example in http://en.wikipedia.org/wiki/Fisher's_exact_test   Men Women Dieting 1 9 Non-dieting 11 3 Using Fisher's exact test I can know whether the proportion of dieting in women is significantly h ...
fisher's exact test control written 4.0 years ago by billzt20
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The relationship between DNA sequence divergence and recombination rates?
... The recombination rate between two sequences falls  as their degree of divergence increases. I hope to know the general quantitive relationship between them in mamalian, especially the threshold: under which divergence can two sequences fail to recombine? I searched some literature but most of them ...
sequence divergence recombination written 4.4 years ago by billzt20 • updated 13 months ago by Hussain Ather910
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The -M options of cufflinks
... Cufflinks has an option of -M <mask.(gtf/gff)>,  which could be used to mask certain transcripts. However, I still found many transcripts having some levels of FPKM after masking, some even reach ~200 Besides, the file "skipped.gtf" in my output directory is blank!. Obviously, something was wr ...
mask cufflinks rna-seq written 4.4 years ago by billzt20 • updated 4.4 years ago by Angle4590
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Comment: C: Extremely large difference between two sample sizes of Mann–Whitney U test
... Thank you. I'll try it ...
written 4.4 years ago by billzt20

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Extremely large difference between two sample sizes of Mann–Whitney U test

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